Sequence
atgc intronic sequence ATGC exonic sequencegtctttgccctttcttcttttcacttttgttttgcttttggacttgccgtgtaacccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
Basic information
species | Glycine max |
transcript | GLYMA01G43650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------gtctttgccctttcttcttttcactttt---gttttgcttttggacttgccgtgtaacccttttataat---ttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
||| | |||| ||| | ||| |||| | || || | |||| | |||||| ||||||||||| |||||||||||||||||||||| | |||||||| ||||||||| |||| |||||||| ||||| ||| ||||||| |
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
---------gtctttgccctttcttcttttc-acttttgttttgcttttggacttgccgtgt--aa--------cccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
|| |||| ||| |||| | | ||| | | ||| || |||| |||| || |||| || |||||||| |||||||| |||||||| ||||| || || ||||| || ||||||||||| |||||||| ||||| | ||| |||||||| |
gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------gtctttgccctttcttcttttcacttttgttttgcttttggacttgccgtgtaacccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
| |||| | | ||| | ||| | || ||||| | ||| | | || || |||||||||||| |||||||||||||| || |||||||| || || ||||||||||| || || |||||||| |||| ||| || ||||||||||||||||||
gtatcctttcttgattttctagtcatacattacctaacactgcatttttgagaataaagactgattcttctattt-attatttgactt--catgtcatc-ttccattcgttagGTTGTCAACATGGAATGGGGAAATTTCTGGTCATCACATTTGCCAAGAACATCTTACGATATTGATTTAGATGGTGATAGTCCTAATCCAAATGATCAG
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S401_23V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------gtctttgccctttcttcttttcacttttgttttgcttttggacttgccgtgtaacccttttataatt--tagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGAT-TTGGATGCTGAGAGCCCTAATCCAAATGATCAG
| | | | | | | || | || | | || | | || |||| |||||||||| |||||||||||||||||||| || || || | || || || | | |||||| ||||||| ||||| || |
actgctctcgtgtaggatatgacttggaatttcgggtgggtttgaatattgaccacgtacccttacataacaagtgatatatggttcctgaccttggcagGTGATCAATATGGAGTGGGGAAACTTTTGGTCATCACATTTGCCTCGGAC-CTATGTGGATGAGTTATTGGATAGCGAGAGCCTCCATCCAGGAGAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttcacttttgttttgcttttggacttgccgtgtaacccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
gtgtaac putative branch site (score: 3)
cccttttat CT-rich tract
ttttataattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttgccctttcttcttttcacttttgttttgcttttggacttgccgtgtaacccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG