Sequence
atgc intronic sequence ATGC exonic sequencegtgtagtgggaataagttctgaatcctgattcttgcatttgaggttaatatcattggatatatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
Basic information
species | Glycine max |
transcript | GLYMA13G17610.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 21
--------------gtgtagtgggaataagttctgaatcc-tgat---tcttgcatttgaggttaatatcattggata-tatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
|| | | || | | | |||| ||| | || | | | || ||||| ||| || || |||| || || || || || || |||| || || || ||||| ||||||||||| ||||||||| ||||||| ||||| ||||| || | || ||||| || ||||||||||| ||||
gtatgtccatatgcatgaattttgacacatctataaatctatgaaatgtaatgatctggtgtttcttatcaaatgatgctacatataaaaactttgctgga-----tgtacat-gtagTTGATCAAGTCAAAAGTTGGCAGCATAAAGTCAGGGTGGCGTTGTGTATTCATGATATTTACTGCAGCGGCTGATGACGAGGATGAATCAATTGTTGAGA
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 23
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 22
-gtgtagtgggaataagttctgaatcctgattct----tgcatttgaggttaatatcattggata-tattta-ctaaaattt----agccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
|| || |||| || || | | || | |||| | | | | | || ||| | | | |||| ||| | ||| |||||||||||||||| |||||||| || || || || ||| | ||||| |||||||| |||||||| |||||||||| ||| | ||||| || || || |
gttgcttgcttgatctattctatattctaaaattaatatgtttccttggtttttgttactcggtagtatgcagccattatttcagcagctaatcaatctttttattttagATGATAAAATCTAAAGTTGGAAGTATCAAATCGGGATGGAGGAGTGTTTTTATGATATTTACAGCAGCTGCAGATGACGAAGTTGAATCGATAGTTGAAA
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 23
---------------------gtgtagtgggaataagttctgaatcctgattct-------tgcatttgaggttaatatcattggatatatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
| | | ||| | | | | ||| || | || ||||| | || | || | ||| || | | | || || || |||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |||||||||||||||||| |||||||||||||||||||||| ||||| || |
gtatgtttatttgattttcctaactgttagtcatatatctctattagttatttgccttaaatgtctctgcatttaatgataacagacagtttcatcaaagtt-aactgaagcttatgt-tagcacagATGATAAAATCAAAGGTTGGAAGCATAAAATCTGGATGGCGTAGTGTGTTTATGATTTTTACAGCTGCTGCAGATGATGAATTGGAATCTATTGTTGAAA
upper sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 23
lower sequence: PP1S19_33V6.1 (Physcomitrella patens), 3'ss of exon 16
---gtgtagtgggaataagttctgaatcctgattcttgcatttgaggt---taatatcattggatatatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
| || ||| | | | | | || | ||| | | || | | | || | | | | | | || || | |||||||| ||||| |||||||| ||||| || ||||||||||| ||||| || ||| | || | | || ||||| ||| ||| || | | |
ctggacgagctggagtgcgatgttgtgtgaatattctgtgatgaaggaacgcgagagcacttgg-ggagatatctgattctgagcagta-tgatgttt---tcagATGATCAAATCGAAGGTTGGGAGCATTAAATCTGGGTGGCGAAGTGTGTTCATGTTCTTCTCCTTAACCGCGTATGATAGTGTGGTATCCATAGCTAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatcattggatatatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
tactaaa putative branch site (score: 1)
atcattggatatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtagtgggaataagttctgaatcctgattcttgcatttgaggttaatatcattggatatatttactaaaatttagccggcactgttgcctatcacagATGATAAAATCTAAGGTTGGAAGCATAAAGTCTGGGTGGCGTAGTGTATTTATGATTTTTACAGCTTCTGCAGATGATGAATTGGAATCAATTGTCGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG