Sequence
atgc intronic sequence ATGC exonic sequence...ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
Basic information
| species | Glycine max |
| transcript | GLYMA12G04290.2 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 2
ggtggagaagattttgatg---tgctatgtacatcatgtgaaaggggagggttttgctt-tatacaatttacagcttt-tgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
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-gtatatataattcggaatcattgttagtgaaatcgtataagctcaaaagaatggatctatacatgatttgttgcattacaatgatgttgatcttgatattgcagGGGATGATTACAAGATTAAAGTGTGGAACTACAAAAACCACAGGTGCCTTTTCACTCTTCTAGGGCATCTTGATTATATCCGCACGGTTCAGTTCCATCA
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
-------ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
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aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcat-atgtagttgatggcatt-gattacattggatgtt-----gcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 2
ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttata-caatttacagcttttg------actatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
||||| | ||| ||| | | | | | || | | || |||||| | || || | | ||||| || || |||| |||||||||||||| ||||| ||||| |||||| | ||||||||||| || || ||| | |||||||||||||| ||||| || || || ||||| ||
-------ggaattttatggggctggacccataagataatatatttgtgtgcctgtgtgtatcaatttttggtttatgcaaatgatggttttttggttattttttcagGAGATGATTACAAGATCAAGGTGTGGAATTATAAGTTACATAGGTGTTTATTTACCCTTTTTGGACACCTTGATTACATCCGCACAGTTCAGTTTCACCA
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S86_189V6.1 (Physcomitrella patens), 3'ss of exon 1
ggtggagaagattttgatgtg-ctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttg-actatattttgtttcttgggac--agGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
|| ||| || || || | | || | ||| | | || ||| | || | | | | | | | | | | |||||||||||| ||||| ||||| |||||||| ||||||| | || ||||||||| | || || ||||| ||||| ||||| || || |||| |||||
----taggctgctttcatctggttagattttctaggtttttttgctaaacttttgtcattctttttaacatggtgtgcaatgtgtatggatattggaaatgtagGGGATGATTATAAGATCAAGGTATGGAACTACAAGATGCGACGCTGCTTGTTCACTTTGCTGGGTCACCTCGATTACATCCGGACGGTCAAATTCCATCA
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
--ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttataca-atttacagcttt-tgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
| | |||| | | | | | || | | | ||| | | ||| || || || || | ||| || || | ||||||||||||||||||| ||||| |||||||| ||||||| | ||| |||||||| | | || ||||| ||||| ||||| || || ||||| |||||
ttattatgcctggttttacttggtgggattccctaggtt---cgtgtgatcttttcatcgtacctatataaagtttaataactgtagga-attgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
upper sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S11_79V6.1 (Physcomitrella patens), 3'ss of exon 1
ggtggagaagattttgatg-tgctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttgactatattttgtttcttgggac--agGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
| | | || |||| | | |||||| || |||| | | || || ||| | ||| | | ||| | | || | ||||||||| |||||||||||||| ||||| || ||||||| | |||||||| ||| | | || || | || |||||||| || |||||||| || ||
gattacccacatattgaagatattatgtagattttgtgtgcgatgcccacttaatttgtattaatattgtgctcta---cgtgtttgggaaccgggaatgtagGGGATGACTACAAGATTAAGGTGTGGAATTACAAGATGCGGCGCTGTTTGTTTACTTTGTTGGGTCATTTGGACTATATCCGGACGGTGCAATTCCACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggttttgctttatacaatttacagcttttgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
ttttgac putative branch site (score: 3)
ttttgtttctt putative PPT
tttatacaatttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttatacaatttacagcttttgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA
ggtggag
- - - - - - - tgatgtg
- - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - - - -gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg
