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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG

Basic information

species Zea mays
transcript GRMZM2G375504_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactg-tgtacaatgttattttgtttggagttcaatgat--gattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG
                          |   |||  ||  ||  | |  |   |   |||  ||    |  ||||  | | | || || |||||  | ||    |     |   ||||   |||   || || ||||| | ||  |||||| |||||  |||||||||||||||||||||||||| |||||  |||||||||||||||||||||||||||||||||| |||
-------------------------gtatgtttaaac-attaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttct-caatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG

upper sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 17
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG
                                                |   ||    |||||    | |||          | |   ||||| | || | |||    |    |    |||| || |   |  | |  ||    | ||         |||||||||||| ||||| ||||| || ||| |||| | ||||||||||||||||||| | || ||||||
------------------------------------------------ttacttccagaatgttagctttttaaa-------tatacgcaatgctgttgtctttcacatcttgtttacattggtagcaagtaatgtggtttgtgtatat-----tggcagTGCTGCTGTCTTTCACAATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG

upper sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 17
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG
                                                        || |  | |  || | ||        | ||   ||| ||||  |   | |      ||  |  |    ||||     | |   ||| |    | ||  |||||||||||| || || |||||||| ||||| ||||| | |||||| || ||||||||| | ||||| |||
--------------------------------------------------------tacaaatgcaatggtctgtaaattgtt-tgagtaat-ttatgctaaattgttgcacatatttgtgttaaccttgaaatgtggctcattat--ctatctcaacagTGCTGCAGTTTTCCATAATGCAAGTACCCGATTTTGTGATGGAGCACGTTTTGGACTTGGTGCAGAG

upper sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
lower sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG
                                                |   || ||    |  || | |||||   |  |   ||| |     |||| | ||  |  |    | ||  |||  || | |  | ||| | |  | || || ||||   ||||| ||||||||||||||||| ||||| || || |||||||| |||||||||||  | ||||| |||
------------------------------------------------taccttcattg-cgctctctcttttgcttgtaatactgttcg----tattgtattcaggct---gtcattgttgtaacattaaataatactgc-ttgcttcatttgc---agTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG

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|19436126|gb|BM952536.1|BM952536
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGT
EST: gi|67010794|gb|CO439543.1|CO439543
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|5804676|gb|AI979646.1|AI979646
EST:     ATGATAAAGTAGCAGAAACTTTTNTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACNCGATTCTCTGATGGGGCTCGTTT
genomic: ATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|20507077|gb|BQ279475.1|BQ279475
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|22491554|gb|BU051477.1|BU051477
EST:     TCACCACAGATGATAAAGTAGCAGAAACTTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: TCACCACAGATGATAAAGTAGCAGAAACTTTT-CTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|60357258|gb|DN224231.1|DN224231
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|60348148|gb|DN215121.1|DN215121
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCG
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCG
EST: gi|211167560|gb|FL481146.1|FL481146
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|71317103|gb|DR795235.1|DR795235
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|60400958|gb|DN233765.1|DN233765
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|87154005|gb|DY398794.1|DY398794
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|67017995|gb|CO446744.1|CO446744
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|211356650|gb|FL094996.1|FL094996
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|6827642|gb|AW331285.1|AW331285
EST:     ATCACC-CAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|32944835|gb|CF049654.1|CF049654
EST:     ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: ATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|6601839|gb|AW256280.1|AW256280
EST:     CAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: CAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
EST: gi|60337963|gb|DN204936.1|DN204936
EST:     GTAGCAGAAACTTTTCTGCGTCAAGTTGTTAG                         TGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT
genomic: GTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTT

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: 244

TGCACATACAGATTGCATTATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 229

TGCACATACAGATTGCATTATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

TGCACATACAGATTGCATTATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 218

TGCACATACAGATTGCATTATCACCACAGATGATAAAGTAGCAGAAACTTTTCTGCGTCAAGTTGATAGgtacgttacc ... attgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG
                   acctgat  putative branch site (score: 218)
                        atgttatattt  TA-rich tract