Sequence
atgc intronic sequence ATGC exonic sequence...ggatgtaatttacgtgggtgaagtttgcacgcattaatttcttgtttcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
Basic information
species | Glycine max |
transcript | GLYMA02G46280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
ggatgtaatttacgtgggtgaa-gtttgcacgcattaatttcttgtttcatgaaaacacat---ttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
|||| || | | | | || || | | | | ||| | | ||| |||||| | | || | || || | |||| |||||||| ||||||||||| ||||| ||||||||||| |||||||||||||| || | || ||||| || ||||| ||| || || ||||
----gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttgtactttat--gtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
upper sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
----ggatgtaatttacg-tgggtgaagtttgcacgcattaatttcttgtttcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
||| | || || || ||| | | | | | | || |||| | || || | | || | | ||| | |||| ||||| | |||||||||||||||||||||||||| || |||||||||||||| || || || || |||| |||||||| ||||| ||| |||| |||||
tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaat----gtttgaccattggccgatcttaatccactata-cagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
upper sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S246_89V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------ggatgtaatttacgtgggtgaagtttgcacgcattaatttcttgtttcatgaaaacacatttacgtgt---taattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
| || | | | | |||| | || | || | ||| | | | || | || | || | ||| || || | | |||||| || |||||||| |||||||| ||||| ||||||||||| |||||||||||||| || | || ||||| || ||||| | | |||| ||||
gtgagaacttggagttctttaaatacttcaacagctactctcatcgcattgcttttgta-gcttcaaagccagctttaagcagttgatatgtgtaagtccctggattaacatggtgagatattttgttttcagATTAACGACGGATGCCAGTGGAGAAAATATGGTCAGAAGATGGCTAAAGGGAATCCTTGCCCTCGCGCATATTACCGCTGCACTGTTATGTCTGGCTGTC
upper sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------ggatgtaatttacgtgggt---gaagtttgcac-gcattaatttcttgtt-tcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
| | ||| | | || | |||| | ||| | | ||| | || | || | | || | | ||||| || | | |||| || |||||||| ||||| || ||||| |||||||||||||||||||| || || || | || || || || ||||| | | || ||||
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatttatctgttttagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
tgttaat putative branch site (score: 3)
atgaatttattataac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggatgtaatttacgtgggtgaagtttgcacgcattaatttcttgtttcatgaaaacacatttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC
- - - - - - -gtgggtg
- - - - - - - - - - - - -tgcacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggga