Sequence
atgc intronic sequence ATGC exonic sequence...gattttttttttaatgatctttgaaatttattttgtcatcccaactcttgcttcctttttttttgaactacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
Basic information
species | Glycine max |
transcript | GLYMA02G40490.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G58270.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------gattttttttttaat---gatctttgaaatttattttgtcat-cccaactcttgct--tcctttttttttgaactacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
| ||||||| | | | || ||| | || | |||| | | || || || | | | || || | | |||| ||||||| | ||||||||||||||| |||||||| |||| ||||| ||||||||| | ||||| ||||||||| | || |||| | ||| | ||| ||| | ||
gtaaagcttgtctgaccacttggtgctttctcatgatcattgttttttttctcattttgaataattggcagttgctcattcatatttggatttcactattcattcgtctctaaaaacactcgacgtaattaatatgtatct-ttcagATATCTATGGTATCAGGTATACTGGCATACAAGTTTGGAGCTGCTTTTGCCTGGATTACTTCTCTCTCCGTTGGATCATATATCGTTTTCACATTAGCTG
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S209_119V6.1 (Physcomitrella patens), 3'ss of exon 8
gattttttttttaatgatctttgaaatttattttgtcatcccaactcttgcttcctttttttttgaactacttcagcagatttaacatgtatcc--------atccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
| | | || |||| | ||||| | | | ||| | || || | | | || | | ||| | || |||| | |||||||| ||||| || || ||| |||| ||||||||||||||||| ||||| ||| || || | | || ||||| ||| | ||| ||| || ||
------agtggtgtcactgttagaaactgtaattgtcttaaataattttgata--ttggttatgaaggcagtttcaaaaacttagcttgcatcctgctttttgtgcagATATCAATGGTGGCTGGAATACTGGCATACAAATTTGGAGCTCCATTTGCATGGATCACGTCTCTTACCGTGGCTGCTTATACTCTTTTCACATTGTCTG
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S249_41V6.1 (Physcomitrella patens), 3'ss of exon 8
----gattttttttttaatgatctttgaaatttattttgtcatcccaactcttgcttcctttttttttgaactacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
|| || ||| | | | | |||| | ||| | | ||| | | | | | ||| | || | | | |||||||| |||||||| || ||| | ||||||||||| |||||||| |||||| ||| || ||| | |||| ||||| || | ||||||| |||||
gagtaatggcattattagaaagcat--agatttccgtaa--atctcctgttttgttctggcgcagcgtcgaatttcttagcttacataccgcattctgttgcagATATCGATGGTAGCTGGGATACTAGCCTACAAATTCGGAGCTCCATTTGCGTGGATCACCTCCCTCACTGTGGCTGCTTACACTCTTTTTACATTGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgcttcctttttttttgaactacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
atttaac putative branch site (score: 3)
tccatcc putative PPT
tttttttttgaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattttttttttaatgatctttgaaatttattttgtcatcccaactcttgcttcctttttttttgaactacttcagcagatttaacatgtatccatccagATATCTATGGTAGCAGGTATATTGGCCTACAAATTTGGAGCTCCCTTTGCGCTGATTACTTCCTTATCTGTTGCTGCCTATGTTACTTTTACACTGACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - -tgtcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcagc