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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgtttttatctgcttctggtgctgtttcagtcccttggtgcatcccttgtagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATTCCAACTGCTGCCGGTGGAGGGGGAGCTAAATGAGCTTTTGATCACTTAT

Basic information

species Zea mays
transcript GRMZM2G368908_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 9
gttggttgtttttatctgcttctggtgctgtttcagtcccttggtgcatcccttgtagatt-ttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATTCCAACTGCTGCCGGTGGA-GGGGGAGCTAAATGAGCTTTTGATCACTTAT
                                                      ||| ||| ||  ||||||      |||||  |      |||       |      | ||     |||  | | |      |   ||  | |||||||||||||||||||||||||||||||| || ||||||||||| ||| ||||||| || | |||||| ||  |  |   | |||  ||  || || |||     | 
------------------------------------------------------gtaaattgtttctgtcttatc--tattgaatatagaagatgcgggagttaggagatactt--gtcatttattgtaagacttccttttatttgattccagATGCTAAACAAGGAGCATGAGAAAGCCGAGGATTCGAAGCCAACCGCCATACCTAGTGCTGCTGGGAGCTGAATGTGCTTTATTTGCCTTAGATTTTGGA-
















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|16745925|gb|BM032355.1|BM032355
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|32942736|gb|CF047555.1|CF047555
EST:     GATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: GATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18384637|gb|BM417836.1|BM417836
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18384913|gb|BM418112.1|BM418112
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACANGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|60340869|gb|DN207842.1|DN207842
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|60355241|gb|DN222214.1|DN222214
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|60399723|gb|DN232533.1|DN232533
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTTGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|16746047|gb|BM032477.1|BM032477
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18384914|gb|BM418113.1|BM418113
EST:     ATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: ATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|88755237|gb|DY539378.1|DY539378
EST:     TTTTTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTGGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|78089023|gb|DV517416.1|DV517416
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCCCAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCCCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|211028541|gb|FL445307.1|FL445307
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18383928|gb|BM417128.1|BM417128
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|108824177|gb|EC278185.1|EC278185
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18384504|gb|BM417703.1|BM417703
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|32857775|gb|CD997456.1|CD997456
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|211046828|gb|FL451687.1|FL451687
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|32938917|gb|CF043736.1|CF043736
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|87153027|gb|DY397816.1|DY397816
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|32934297|gb|CF039109.1|CF039109
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAACCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|18384506|gb|BM417705.1|BM417705
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|16925720|gb|BM078788.1|BM078788
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|78089024|gb|DV517417.1|DV517417
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|161585959|gb|EY955356.1|EY955356
EST:     CGGAGTGTCATTGCCCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
EST: gi|110520623|gb|EE024807.1|EE024807
EST:     CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG                         ATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT
genomic: CTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtt ... gtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATTCCAACTGCTGCCGGTGGAGGGGGAGCTAAATGAGCTTTTGATCACTTAT
                                  tgttaat  putative branch site (score: 3)
                                  tgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttgtttttatctgcttctggtgctgtttcagtcccttggtgcatcccttgtagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccagATGCTAAACAAGGAGCATGAGAAGGCTGAGGATTCGAAACCAGCCGCCATTCCAACTGCTGCCGGTGGAGGGGGAGCTAAATGAGCTTTTGATCACTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT