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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgatctgcttgatgttataaattttcattcttcggcgcaaacttgacgaacctgggcatgacttactattttcttatcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC

Basic information

species Zea mays
transcript GRMZM5G823629_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
tatttgatctgcttgatgttataaattttcatt-cttcggcgcaaacttgacgaacctgggcatgacttactattttcttatca-catgt-tttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
|    ||| |  ||    ||||||  | |  || |   | |    |||      | |  |||| | | ||  |||||||| |   ||| |   | | ||  ||||||| ||| |  |||||||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||
tggaggatatatttt---ttataatctgttgttgccatgaccattactatttttatcgtggcagggcctaacattttctttttttcatctacctgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC

upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
tatttgatctgcttgatgttataaattttcattcttcggcgcaaacttgacgaacctgggcatgacttactattttcttatcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
|||   | | |        |     |       |||   |  |  | | ||         |  |   || |  |||||| |    |   ||  ||| |||||||| || || |||||||||| |||||| |||||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||||
tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
tatttgatctgcttgatgttataaattttcattcttcg---gcgcaaacttgacgaacctgg-gcatgacttactattttcttatcacatgtt--ttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
          | |   | | |    |||||  |  ||    | |    |    |||  ||   | ||   |   | | |||  || || || |  |   | | ||| | |||||     | ||||||| ||| ||  | ||||| || || ||||| ||||| |||||||| ||||||||||| || || ||||||||||| ||||
-----agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattca-ataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC

upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
tatttgatctgcttgatgttataaattttcattcttcggcgcaaact-tgacgaacctgggcatgacttactattttcttatcacatgttttc---cttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
   ||  |   ||| |      |  | |   | |||  |  |||||  ||  | || |       |   ||| | |||  | |  ||||        | | ||| | |||||     ||||||||| ||| ||  |||| || || |||||||| ||||| |||||||||||||||||||| || ||||||||||| || || |
--cttagttaactt-acaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaact-tattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC

upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT4G39390.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------tatttgatctgcttgatgttataaattttcattc--ttcggcgcaaac-----ttgacgaacc----tgggcatgacttactattttcttatc--acatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
                                                                         | |  | |   |  |  ||  ||||  ||||   | |  | |||       |||    ||     |||   || ||| |        ||||  |||   |||  |   ||||||||  |  |  | |||||||  || || |||||||| ||||| ||||||||||| || || ||||||||||| || || || |||||||| || || |
gtaaagtttcttctccgtttctttacaaagtctcctacgattcaaaacagagcaatgagtatttggaacatagtgtagtattagtagtcataccaattcgcatttattccatctcaagaactgattgttatactctgttggatttgtctttcctaagctctatctaacacaattttttgggcagTTCTTCTTAATACTCTCGTGCAGTATCGCGGTTGGGACCAATCTCAGCCAATTCATCTGTATTGGAAGATTCACGGCGGTGTCTTTCCAAGTACTTGGTC

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|78079408|gb|DV507820.1|DV507820
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTTACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCG
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCG
EST: gi|71445237|gb|DR826287.1|DR826287
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTTACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGT
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGT
EST: gi|78079407|gb|DV507819.1|DV507819
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|71445236|gb|DR826286.1|DR826286
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|60337491|gb|DN204464.1|DN204464
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|67020229|gb|CO448978.1|CO448978
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|67012439|gb|CO441188.1|CO441188
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|76281273|gb|DV020841.1|DV020841
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|31364467|gb|CD448822.1|CD448822
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTG
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTG
EST: gi|32941721|gb|CF046540.1|CF046540
EST:     ATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: ATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|37401537|gb|CF638135.1|CF638135
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|76015509|gb|DT942679.1|DT942679
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
EST: gi|76280569|gb|DV020137.1|DV020137
EST:     GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACG                         TTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA
genomic: GGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgata ... tccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacgaacctgggcatgacttactattttcttatcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC
                  gacttac  putative branch site (score: 2)
                                      catgttttccttttc  putative PPT
                     ttactattttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgatctgcttgatgttataaattttcattcttcggcgcaaacttgacgaacctgggcatgacttactattttcttatcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - -tgcttga
- - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt