Sequence
atgc intronic sequence ATGC exonic sequence...gtacattggtataataagttatttattgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
Basic information
species | Glycine max |
transcript | GLYMA11G12080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 1
gtacattggtataataagttatttattgtccatgtggaaggggagggctttgcttta-tacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
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-catactggtgtccggtcgtattgctcggtggactaatatgattgggatgcggaatggttgaacttctgaactattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCACGGGCACCTTGACTATATTCGCACCGTGCAATTCCACCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 2
------gtacattggtataataagttattta-ttgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
|| | || || || | | | | || | | || | | || | | || | |||| || | | || | || | |||||||||||||||||||||| || |||||||| || | || |||||| | |||||||||||||| || |||||||||||||| || || || || |||||
gtatatataattcggaatcattgttagtgaaatcgtataagctcaaaagaatggatcta---tacatgatttgttgcattacaatgatgttgatcttgatattgcagGGGATGATTACAAGATTAAAGTGTGGAACTACAAAAACCACAGGTGCCTTTTCACTCTTCTAGGGCATCTTGATTATATCCGCACGGTTCAGTTCCATCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacattggtataataagttatttattgtc-catgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
| | | || || | || || | || | | | ||| || | | || | || | | || || || |||||||||||||||||||||| ||||||||||| || | || ||||| | ||||||||||| || || |||||||||||||| || || |||||||| ||
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactca-tatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtacattggtataataagttatttat-tgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
| | || |||| ||||| | || | |||| | |||| ||||| ||| | | | || ||| ||| | || |||| |||||||||||||| ||||| ||||| |||||| | |||||||| || || || ||| | |||||||||||||| ||||| || || || ||||| ||
ggaattttatggggctggacccataagataatatatttgtgtgcctgtgtgtatcaat----ttttggtttatgcaaatgatggttttttggttatttttt-----------cagGAGATGATTACAAGATCAAGGTGTGGAATTATAAGTTACATAGGTGTTTATTTACCCTTTTTGGACACCTTGATTACATCCGCACAGTTCAGTTTCACCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S86_189V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacattggtataataagttatttattgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggac--agGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
|| || | | || | | | ||| || | || | |||| | | || ||| | | | | | ||| | | | | | |||||||||||| ||||| ||||| |||||||| ||||||| | |||||||||||| | || || ||||| ||||| ||||| || || |||| |||||
-taggctgctttcatctggt-tagattttctaggtttttttgctaaacttttgtcattctttttaacatggtgtgcaatgtgtatggatattggaaatgtagGGGATGATTATAAGATCAAGGTATGGAACTACAAGATGCGACGCTGCTTGTTCACTTTGCTGGGTCACCTCGATTACATCCGGACGGTCAAATTCCATCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacattggtataataagtt--atttattg---tccatgtggaaggggagggctttgctttataca-atttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
|| ||| ||| | || || | | || | | | |||| | | ||| || || || ||| | ||| || || | ||||||||||||||||||| ||||| |||||||| ||||||| | || |||||||| | | || ||||| ||||| ||||| || || ||||| |||||
-----ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtagga-attgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
upper sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S11_79V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacattggtataat-aagttatt-tattgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggac--agGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
| | ||| | ||| |||| | | | |||| | | ||| ||| || || | | | | | | | | | || | ||||||||| |||||||||||||| ||||| || ||||||| | || ||||| ||| | | || || | || |||||||| || |||||||| || ||
gattacccacatattgaagatattatgtagattttgtgtgcgatgcccactt-aatttgta---ttaatattgtgctctacgtgtttgggaaccgggaatgtagGGGATGACTACAAGATTAAGGTGTGGAATTACAAGATGCGGCGCTGTTTGTTTACTTTGTTGGGTCATTTGGACTATATCCGGACGGTGCAATTCCACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
tattgac putative branch site (score: 2)
ttgtttctt putative PPT
ttattgactatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattggtataataagttatttattgtccatgtggaaggggagggctttgctttatacaatttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA
- - - - - - - - - - - - - - -ccatgtg
- - - - - - - - - - - - - - - - - - - - gggaggg