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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT

Basic information

species Zea mays
transcript GRMZM2G034083_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 6
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctcct-tgaagta-attatt--tcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccac-tagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT
                         | || |   ||| |   ||||| ||| ||||||    |     | | |    |    ||| ||||  ||    ||| | ||| | || |   |||| |||    |  | || |   | | |||      | |  | || ||||||||  | || || |||||||| || |||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||| || || |||
------------------------gtaacctcatatttctttctttcccctctgaagtctgctgcctgttagtacatatcacttaaatttggatacaaattgaatttcactgcc---tctgcatgcaaaatattgaatcttgaattgaggttgatgtaatttttcagACAAGCTCATCGCTCAAATTCACAGTCCTGAACCCGAAAGGGCGCATTTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATATGCTGATACT

upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT
                              |  |  |||| | |||||     ||  |    |||  |    |||     | |     | ||| |   | | ||| ||||  |||   ||||     |   | |  ||  |        |  ||| |||||||||||||||||| |||| ||||| ||  |||| || ||||| ||||| ||||| ||||| || || ||||||||||| |||||||| || || || 
---------------------------gtttaagcatccagcttttcta---aaaacaccacttttgtgactcagacaggaaag----acttgaaagtaatgttactgaccattc---atgtctgtgtgtgtgtgtgtgtttg------ttacttattgcagACAAGTGCTTCTTTGAAGTTCACTGTTTTGAATCCTAAAGGCCGCATTTGGACGATGGTAGCTGGAGGTGGTGCTAGCGTCATATATGCTGATACA

upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 7
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT
                                                            | | |  |||||      | | |||  | | |  | | |     ||||    ||   ||||| |  |   |  | |      ||   |||    |  ||||||||||||| ||| |||| ||||| ||  ||||||| ||||||||||||||||| ||||| || || |||||||| ||||| ||||| || || |||
------------------------------------------------------------tttctggttttctcaatctaagattagtctgttcaatcatagaaattggagtttacctatgtacagcagaaagtgatccactaat--cttacactggtgcagACAAGTGCATCTTTGAAGTTCACTGTTTTGAACCCCAAAGGACGCATCTGGACTATGGTAGCTGGAGGTGGTGCAAGTGTTATATATGCCGATACT

upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT
                          |    | |||||  |  | |||  |  |||  | ||    ||| | |    |  | | || ||        || |    || ||       | | |       |  ||||||||||      || | |   |||||||  |||||||||||||||| ||| ||||||| || || || ||||| |||||||||||||| || |||||||| |||||||| ||||| || |||
-------------------------gtgtgattgattc--atttatctaatacaagacactaccaaattcttccac-tccagactt-taaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtg-----tttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32848515|gb|CD988196.1|CD988196
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTA
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTA
EST: gi|67023264|gb|CO452013.1|CO452013
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|40303556|gb|CK347943.1|CK347943
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|31357444|gb|CD441801.1|CD441801
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67013475|gb|CO442224.1|CO442224
EST:     GAAGAGTTCTCACTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|211020101|gb|FL063974.1|FL063974
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|18964714|gb|BM661164.1|BM661164
EST:     GAAGAGTTCTCAGTCCCTCCG-AAGTTTTATCCATGAACTGGATGAGATG                         AC-AGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|60353107|gb|DN220080.1|DN220080
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGCGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|18964715|gb|BM661165.1|BM661165
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|22490798|gb|BU050721.1|BU050721
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67025367|gb|CO454116.1|CO454116
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67010398|gb|CO439147.1|CO439147
EST:     AGAGTTCTCAGTCCCTCCGAANAGTTT-ATCCATGAACTGGATGAGAAAG                         ACA-GTGCTTCTCTGAAAT-CACGGTACTGAACCCAAA-GGACGCATCTG
genomic: AGAGTTCTCAGTCCCTCCGAA-AGTTTTATCCATGAACTGGATGAGAA-Ggtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTG
EST: gi|7238111|gb|AW573333.1|AW573333
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|44901489|gb|CK828034.1|CK828034
EST:     GAAGAGTTCTCAGTCCCTCGGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGT
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|149008522|gb|EE040695.2|EE040695
EST:     CCATGAACGGGATGGGAAG                         ACAAGTGCTTTTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: CCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|19058295|gb|BM736962.1|BM736962
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         CCAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|78103680|gb|DV522108.1|DV522108
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|31353311|gb|CD437668.1|CD437668
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|13150060|gb|BG320382.1|BG320382
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|37400570|gb|CF637640.1|CF637640
EST:     CCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: CCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|31354936|gb|CD439293.1|CD439293
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|60339101|gb|DN206074.1|DN206074
EST:     G-AGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|19057819|gb|BM736486.1|BM736486
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|84980549|gb|DW530898.1|DW530898
EST:     GAACTGGATGAGAAG                         AC-AGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|87151765|gb|DY396554.1|DY396554
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67042517|gb|CO468772.1|CO468772
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|32859101|gb|CD998782.1|CD998782
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67022701|gb|CO451450.1|CO451450
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|149000524|gb|EE037707.2|EE037707
EST:     AAGAGTTTTCAGTCCCTCCGAAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTTTCTGAAATTCACGGTACTGAACCAAAAAGGACGCATCTGG
genomic: AAGAGTTCTCAGTCCCTCCG-AAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|60350340|gb|DN217313.1|DN217313
EST:     AAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGCGCTTTTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: AAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|33104123|gb|CF064083.1|CF064083
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGT
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGT
EST: gi|166544546|gb|EG308464.1|EG308464
EST:     CTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: CTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|37401585|gb|CF638160.1|CF638160
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCGTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG
EST: gi|67016541|gb|CO445290.1|CO445290
EST:     GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG                         ACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGA-GCATCTGG
genomic: GAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 472

GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 544

GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAGgtatgttcat ... cttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT
 tattgac  putative branch site (score: 544)
                                     ccacttctcttcttgc  putative PPT
                    tagatttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG