Sequence
atgc intronic sequence ATGC exonic sequence...atgggaattgaattgttaaactggttgaactgtctgggataggaatacatctatatctgtttaacttggtgcagaatgttaataaatccctgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
Basic information
species | Glycine max |
transcript | GLYMA02G46780.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 9
atgggaattgaattgttaaactggttgaactgtctggga--taggaatacatctatatctgtttaacttg-gtgcagaatgttaataaatccctgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
|| |||| | ||| | | | | | || | | ||| || | | | || | || | ||| | || |||||||||||||||||||||| | || |||||||| | |||||| ||||||| ||||| || || || ||||| |||||||| ||| | ||
tcaaatccagatttgtgtagggcattgcattctttatgtcttaatgtttcctctg-gtccacatgtcatatatgtaaaaatgtgatattttgtc--ttgacagATTCAATGTCTGTTTGGAACTTGCTAAGAGAGTTTCGCATCAGGCAGGTTCATATGGCAGTGGTCCTCAACGAATATGGTGGGACTATTGGT
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------atgggaattgaattgttaaactggttgaac-tgtctgggataggaatacatctatatctgtttaacttggtgcagaatgttaataaatcc--ctgatttg-cagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
||| | | || | || | | | ||| | | | | | || | | | | | | || | ||| | | ||| | || || |||||||||||||||||||||| || | ||||||||| | |||||| ||||||| ||||| || || || || || |||||||||||| | ||
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtca-tagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 9
atgggaattgaattgttaaactggttgaactgtctgggataggaatacatctatatctgtttaacttggtgcagaatgt--taataaatccctgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
| || || || || || | || ||| | | | | |||| | | ||| | | | | || || | |||||||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||||||||| ||||||||||| || ||||||||||| | ||
gtaatcatagatgcattcaatcttttaatctaat--acatatacctttgacattctttgttca-catggaataatctttgatgttatgtcaataatttgcagATTCGATGTCAGTTTGGAATCTTCTTAGAGAGTTTAGAATAAGAAAGGTTCACATGGCAGTTGTTCTTAATGAATATGGTGGAACCATCGGA
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------------------------------------------atgggaattgaattgttaaactggttgaactgtctgggataggaatacatc---tatatctgtttaacttggtgcagaatgt--taataaatccctga-tttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
|| | ||| |||| | | | | | | | | |||| | || | | || ||| | | ||| | | ||| || | |||||||||||||||||||||||||||||||||||||| ||| |||| || |||||||||||||| ||||| |||||||| ||||||||||| | ||
gtaattatcaatgtgtttgcttttggatatgttgccaaactaggcatttgaatgcttcagattttttctgcattcggattaaattatactgttatattaccgacattaaacacgaattcttcacactgaattattatactctgaagaaaatctaatgatatatgttacactttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAATTCCGAATAAGAAAGGTTCACATGGCAGTTGTCCTTAACGAATATGGTGGAACGATCGGA
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 9
atgggaattgaattgttaaactggttgaactgtctggga-taggaatacatctatatctgtttaacttggtgcagaatgttaataaatccctgattt-gcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
| | | | || | || | || | | | | | | | ||| |||| | |||| || | | |||| ||||||||||||||||| ||||||||||| ||||| || | ||||||||||| |||||||| |||||||| || ||||||||||||||||||||
-ttgtcttgctttcattgatttgaacctaagacctcccactcgccaaataagtgc-tctaaccaactgagctttgaataaacttataacatcaattttgcagATTCAATGTCTGTCTGGAATCTTCTAAGAGAATTTCGCATCAGGAAGGTCCACATGGCTGTTGTTCTCAATGAGTATGGTGGAACTGTGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatctatatctgtttaacttggtgcagaatgttaataaatccctgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
tccct CT-rich tract
agaatgttaataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgggaattgaattgttaaactggttgaactgtctgggataggaatacatctatatctgtttaacttggtgcagaatgttaataaatccctgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - -actggtt
- - - - - - - - - - - - - - -ctgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgca