Sequence
atgc intronic sequence ATGC exonic sequencegtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTCCAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
Basic information
species | Glycine max |
transcript | GLYMA13G18580.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
| | |||||| | || | | |||||| || | | |||||||| | ||| ||| || | | || || | || | ||||||| |||||||| |||||||||||||||| ||||||||| ||||| ||||||| |||||||| | || |||||||||||||| |||||||| |||||
----------------------gtattattccctcctggttctgctattatggcatataatattctgtga---------gaaccaatttatgtac----atgtgatatatgcta--attaatcttttgttgttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
| ||||| | ||||||| || | || | || | | | ||| || | | | || || | || ||||||| |||||||| || ||||||||||||| ||||||||| |||||| |||||||||||||||| |||||||| |||||||| ||
------------------------------------gtacagtttttttttctcgccaaatattcaggaattact---tgatttactatatttttctcaatctgaaaag-------------agGTACCTTTCCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA--------------
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
| | |||||| | | || | | |||| || | | || | || || | | || | || | |||| | ||| | ||| |||| || |||||||| |||||||||||||||| ||||||||| |||||| ||||||| |||||||||| |||||||| |||||||| |||||| | |||||
----------------------gtattattccctcctgcttctcttattatggtgtattttattctctatgatct---tgatatg-ttcaaatc---tgatata-tgaatttccttaccttggcgtt------cagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
| ||||| | |||| | | ||| ||| | || | || | | || ||||| ||| || || |||| | | | ||| | ||||||| |||||||| || ||||||||||||| ||| ||||| || ||| ||||||| ||||| || |||||||| ||||| || |||||||| |||||
------------------------attattccaacttaaaatgtagg--acaaaggaagtagctcagaacttcata-----tatgttttatcttcacgagt-caaaaaatatgaaaacatacacgtt----ttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
|| | | | | | | ||||| | | || || | | | | | | | ||| | || | | ||| ||||| | ||| | |||||||| ||||||||||| ||||||||||||| ||||||||| | || | || ||||||||||||| |||||||| |||||||||||||| ||||||||
--------------gtaatgaccccactcttctttccaaaaagtagtctgc--ctgatcctgtctaaacagacccagttctttggttttttatttt---------catcttctcatatgc-tttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
gtaattgattttttgttagaccttgtcattcccctt-caaaagtttgatagcaatagaaaatattgagtagtttttgg--ctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
|| | | | || | | | | | | | | | | ||| | |||| | || | ||| |||| | | || | | | | ||| || | | | || | | | |||||||||||||||| |||||||| ||||||| |||||| |||||||| ||||||| ||||| || | |||||||| |||||||| ||||||||||||||
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttt-taggctaacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
||| || ||| || || | | || || | ||| | | ||| || | ||| | | ||| ||| || | || || | |||| || || || || |||||||| ||||||| |||||||||| ||||| |||| || || ||||| | ||||| || ||||| |||||||||||||||||
----------------------------------ttcgtg---ttactagtaagttgaagctcttcaaaacttcaggttc-tcttacatgtgt-ctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG--
upper sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ16263 (Selaginella moellendorffii), 3'ss of exon 6
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
||||| ||||| | ||| || ||| | | | | || |||| | | ||| | |||| || ||||||||||| ||||| || | | |||||||||||||| || ||||| || ||||||| ||||| || ||||||||||| |||||| ||||
--------------------------------------------------------------gtgagtgattttttttctttttgacttttgtggcctaga--agtggttttcatt-tcccgaagttgtgct-cagGAGCCAATGATGTCTCCATGATACAGACAGCAGATGTTGGAATTGGATTGAGTGGCCAGGAAGGTCGGCAAGCAGTCATGGCATCTGACTTTGCATTGGG--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|14206275|gb|BG839953.1|BG839953EST: TGCCCTTGTGAAGAATAGAACATCTGACATGACACTAGCCATTGGAGATG GTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCA
genomic: TGCCCTTGTGAAGAATAGAACATCTGACATGACACTAGCCATTGGAGATGgtaattgatt ... tacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTCCAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
gtctgat putative branch site (score: 4)
taataaattccattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTCCAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG