Sequence
atgc intronic sequence ATGC exonic sequencegtaagatagatatctggacggttttatttccaatatttttgttcctacagtgattagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
Basic information
species | Glycine max |
transcript | GLYMA11G14880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtaagatagatatctggacggttttatttccaatattt----ttgttcctacagtgattagctagtacttttcaatttc--tattgatttaccgtg-agtctactgtattgt-aatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
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gtatcatatcaggattatcatttgtttagaaataataacctgctaagtcatttatcaatcttcacagctaattctgaag-gcttgcatgatattcactgacatcactgttgaattgttttttggtctgatgcaatgccaacctttagGCCGGATTTGCAGGAGATGATGCTCCAAGGGCTGTGTTTCCTAGTATTGTGGGTCGTCCACGGCACACTGGTGTGATGGTTGGGATGGGCCAGAAAGATG
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaagatagatatctggacggttttatttccaatatttttgttcctacagt-gattagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
| | ||||||| ||| || || || | || | | ||| | | | | | | || |||| || | ||||||| || ||||| || |||||||| | ||||| || |||||||||||||| || ||| | ||||| ||||||||||| || ||||| || || || |
----------ctcttttgcatctttatttataatgggcagacattggatgtagactaatt--tatgatcaatcctctcgaaactgtgtttaattttggtgaattg-aacgc--agGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagatagatatctggacggttttatttccaatatttttgttcctacagtga-ttagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
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---caattcatgctataatggc---gttcatgataatactattca---agtgacttcagttgtgctgtccagaacgaaaccgtgtt---taattgtggtgaattg-aacgc--agGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gtaagatagatatctggacggttttatttccaatatttttgttcctacagtgattagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
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-------------------------------------------------gtgcgctcctggcgc-----ggtttcttgtggattttgatccggggggtgtgttct----tgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gtaagatagatatctggacggttttatttccaatatttttgttcctacagtgattagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
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-------------------------------------------------gtgcgctcctggcgc-----gatttcttgtggattttgatccggggggtgtgtt----tttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
tattgat putative branch site (score: 3)
ttttcaatttctattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatagatatctggacggttttatttccaatatttttgttcctacagtgattagctagtacttttcaatttctattgatttaccgtgagtctactgtattgtaatgtttagGCTGGATTTGCTGGGGATGATGCTCCAAGGGCTGTGTTTCCCAGCATTGTTGGTCGTCCCCGTCACACGGGAGTGATGGTTGGCATGGGCCAAAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG