Sequence
atgc intronic sequence ATGC exonic sequence...caatcttatatctccacttggcaatgtgtaatgtgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
Basic information
species | Glycine max |
transcript | GLYMA03G00510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
---------------------caatcttatatctccacttggcaatgt--gtaatgtgtgttgtca--tttgctattttggataaaagaattgatatcaggtaccattgattatattct---ttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
| ||| | | || ||| ||| | | | | || || |||| || ||| | | |||| || || | ||| ||| || ||||||||||||| ||| | ||||||||||| |||||||| ||||| ||| ||||||| ||||||||| |
gttggtgcattaatttcaataggtttctatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgtt--cattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
---------------------caatcttatatctccacttggcaatgt--gtaatgtgtgttgtca--tttgctattttggataaaagaattgatat-----caggtaccattgattatattct---ttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
| | |||| | | || ||| ||| | | | | || || |||| || ||| || | ||| || || | || ||| || ||||||||||||| ||| | ||||||||||| |||||||| ||||| ||| ||||||| ||||||||| |
gttggtgcattaatttcaatagatttttatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
-------------------caatct-tatatctccact--tggcaatgtgtaatgtgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
||| | | || | |||| | || | || | || | || || || |||| || | | || | | | |||| |||| || | ||| || ||||||||||||| | | ||||||||||| |||||||| || || ||| ||||||| |||||||||| |
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtg-taatttgcatgtagca--tgctcttaatattcatt--ttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30290.2 (Arabidopsis thaliana), 3'ss of exon 6
caatcttatatctccacttggcaatgtgtaatgtgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
||| | | ||||| | | | || ||| || | | | || || | | | | | || | ||||||| ||||| ||||||||||| ||||||||||| || |||||| | || ||| | | |||||||| || ||||||
---------gtcttctttacttaatgtacattttactttttcacctggttcatgatttttaatgtatggtcttgaattttgt-gtttggacg----acagACATAGAAACCAATGAGTGTTTACAAAACAATGGAGGGTGTTGGGAAGATAAAACAACCAACATTACAGCTTGCAGG
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------caatcttatatctc-cacttg-gcaatgtgtaatgtgtg--ttgtcatttgctattttgg-ataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
| | | | | || || | | || || |||| | | | ||| ||| ||| | | ||| || | | |||| | || || | | |||||||| ||||||| ||||| |||||| ||||||| ||||| || ||||| ||||||||| | ||||||||||||||||||
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagaca----tgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
upper sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
caatcttatatctccacttggcaatgtgtaatg-tgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgatta--tattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
|| |||||| | || ||| | || | || | | | || | |||| ||| | | ||| | |||| | |||| | || ||||||||||||||| |||| |||||||| || |||||||| || ||| |||| ||||||||||||| |
-tatattatattat--ttaggaaataaattgtggtatgaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
cattgat putative branch site (score: 4)
tattcttt putative PPT
ataaaagaattgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatcttatatctccacttggcaatgtgtaatgtgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - -ctccact
- - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa