Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA07G03890.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
gtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
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------------------------------------------------gcataattgatttcttttcttctccagattttgaag--aaaatattcctttttcaaaattttctaataacagt--------tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 18
gtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcatttctaatttgcactagtttgatttgagttt--atattgtgagtaatgctcatcttct---tttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
| ||| ||||| | || | |||||| | | | || ||| | ||| | | || || | || || | | || | | ||| ||| ||| |||||| ||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| | || |||
------------------------------------------gtaatatcata--tgtgatgcttaattgcttagacat-tactttactctactctttttggaagtagaattttttttcttatctttgttttccatgcttgtagGAAATTGCTGAAGAAGTACAGAGCGAGTCTAAATGGAAGCAGTTAGGAGAGTTAGCCATGTCCTCGGGGAAG
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
---------gtaagttcatatgttcctgcaaggatatattatttgactcgtga-aatttcataactctgctatttaa------ttttctgcatttctaatttgc-actagtttgatttga-gtttatattgtgagta----atgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
|| || ||||| | | ||||||| | | | ||| | ||| | ||| |||||| ||| | |||| | | |||| | ||| || ||| | || ||| || |||| || |||| |||||| | |||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||
gtaaattatgttgattt-tatgtcagtatagggatataa-actagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
gtaag----ttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaatt--ttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttctt-ttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
||||| || || | | | | | ||| | | || |||| | | || || | | | | ||| || || | | | | |||| ||| ||| ||| | | |||| ||||||| || ||||| ||||| |||||||| ||||||||||||| |||||||||||||| ||||| | |||||||
gtaagaatttttatttatctttagttaggtgtataaaccttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttcttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAG
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 18
gtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcattt---ctaatttgcacta-gtttgatttgagtttatattg--tgagtaatgctcatcttcttt----tgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
| | |||| || | |||| ||| | || || ||| || | ||||| || || | | |||| |||| | | | | ||| |||| | | |||||| ||||||| ||| || ||||||||||| ||||||||| |||||||||| || ||||| ||||||||
-----------------------gttgtatttttaataacatgaattttgaaaattcattcattatgttcgttacatttagactcggttacgtcaagtttaatttacagatgcactaactagaacatgttcatatgttaaccaatgcagGCTATTGCTGAGGAATCACATAGTGAGTCCAAGTGGAAGCAACTGGGAGAATTGGCAATGTCAGCTGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcactagtttgatttgagtttatattgtgagtaatgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
gtttgat putative branch site (score: 5)
tgctcatcttctttt putative PPT
atttgagtttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA