Sequence
atgc intronic sequence ATGC exonic sequence...tcggttaacataacacctataggttcatgcagaaaataaaaaagccttgttgcttttataaccattgaaatctaatccacttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
Basic information
species | Glycine max |
transcript | GLYMA20G35970.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g37480.2 (Oryza sativa), 3'ss of exon 4
---tcggttaacataacacctataggttcatgcagaaaataaaaaagccttgttgcttttataaccattgaaatctaatccacttatatattttactttcta---gAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
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tacctggctaaagctgcagcaaactgatttttttttaa-caaaatag--ttgc-acctttatga--aatatactctctatcatttaacaagtgaactatctaacagAGTGAATACCAACGAGGTGTTAGTGCATGGAACTTCGATGTTGAAGATCTCAAGGCCCAAGCATCACTA
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G413544_T01 (Zea mays), 3'ss of exon 8
-tcggttaacataacacctataggttcatgcagaaaataaaaaagccttgttgcttttataaccattgaaatctaatccacttatatattttac-----tttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
|| | ||||| | ||| ||| | | | | || | || | || | ||| ||| | | | ||| | | | | ||||||||||||| || || ||||||||||||||||||||||| || ||| | || || ||||| |||||
cacgtgtcacata-tattagtagattccttttgt---tgtagaattttggtaaatgccatggctattttaat--agccttatcataaactgcatggattcatacagAGTGAATATCAACGCGGTGTTAGTGCATGGAACTTCGATATCGAGGATCTCAAGGCTCAAGCATCATTG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G073399_T02 (Zea mays), 3'ss of exon 8
-tcggttaacataacacctataggttcat-gcagaaaataaaaaagccttgttgcttttataaccattgaaatctaatccacttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
|| || || || | | || | | |||| || || || ||| | | | || | | || || | ||||||||||||| || || ||||||||||||||||||||||| || ||| | || || ||||| ||||
gtcaaatatattagcagcattccttttgttgtagaattagggtaaatgccacagccattttaatagctttcttatcataaaactgcatggatt--catacagAGTGAATATCAACGCGGCGTTAGTGCATGGAACTTCGATATCGAGGATCTCAAGGCTCAAGCATCATTA
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G124550_T01 (Zea mays), 3'ss of exon 8
tcggttaacataacacc-tataggttcat--gcagaaa-ataaaaaagccttgttgcttttataaccattgaaatctaatccac---ttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
| || | || | | || ||||| ||| | | || | ||| | | ||| | | | || | || || ||| || | | ||||||| || || ||||| || ||||||||||||||||||||||| ||| | || || || || || ||
------agcacaccatcatgtattttcataggcatagatgcaatatttacttctgtcctttttcatcgatgtgactatttctgaaggttctatggtt-atgtgacagAGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCATCACTG
upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G124550_T03 (Zea mays), 3'ss of exon 2
tcggttaacataacacc-tataggttcat--gcagaaa-ataaaaaagccttgttgcttttataaccattgaaatctaatccac---ttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG-------------------------------
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------agcacaccatcatgtattttcataggcatagatgcaatatttacttctgtcctttttcatcgatgtgactatttctgaaggttctatggtt-atgtgacagAGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCATCACTGGTAAAGGAATATGTTTTCTTATCTTTTATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttgcttttataaccattgaaatctaatccacttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
ttttactttct CT-rich tract
acttatatattttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcggttaacataacacctataggttcatgcagaaaataaaaaagccttgttgcttttataaccattgaaatctaatccacttatatattttactttctagAGTGAATATCATCGAGGAGTTAGTGCATGGAACTTCGATATTGATGATTTGAAAGCACAAGCGGCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - aacataac
- - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactta