Sequence
atgc intronic sequence ATGC exonic sequence...aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatatatgaagtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
Basic information
species | Glycine max |
transcript | GLYMA16G15820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 6
----aaataattatctgtatgtgcatattct-tagaattcattttatttcttgggttcactaaatatatgaagtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
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agaaaaataatgatttcttgcagttttttctgtagaaatctttgtggcattattaatagtttgctatttatta-attgatgcctgttactgtgtcctgcagTCC-TCTAGCCGTTTTGATGAACTACCAGATGAATTAGATCCCATTGGGAAACTTCCAGGATCATTTGATGATGGGGATCCACAAACCACGAACTTATATG---
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 6
aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatata-tgaagtacttctactgatagtt--tttccccttaaacagTCC---AGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
| | || | | || | | | | ||||||| | || | | || | || | | || | |||| | | || |||||| || || ||||| || || || ||||| ||||| || | ||| | | |||||||||||||||||||||||||||||||||| || || | ||||
-actgatgtccagctaatgagaaatttgtgtgatcattttgtagtttctat--atgaattttaatagttttttttcattgatgcctaacattattttgtgcagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG---
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 6
aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatatatgaagtacttctactgatagtttt--tccccttaaacagTCC---AGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
|| | || | | || | | | | ||||||| | || | | || | || | | ||| | |||| || | || |||||| || || ||||| || || || ||||| ||||| || | ||| | | |||||||||||||||||||||||||||||||||| || || | ||||
aactgatgtccagctaatgagaaatttgtgtgatcattttgtagtttctat--atgaattttaatagtttctttcattgatgcttaaaattattttgtgcagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG---
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
---aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatatatgaa-gtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
| | ||| ||||| | || | | ||| || | ||| | | | | || ||| ||||| | | ||| ||| | | | | | || | ||||| |||||||||||||||||||| || |||||||| ||||| ||||||||||||||||||||||| |||||||| ||||| ||||
agtatgcatatatagttatgtttctgttgtctttctgcatcttgcat-ttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgggttcactaaatatatgaagtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
tactgat putative branch site (score: 2)
tagtttttcccctt CT-rich tract
taaatatatgaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaataattatctgtatgtgcatattcttagaattcattttatttcttgggttcactaaatatatgaagtacttctactgatagtttttccccttaaacagTCCAGTCGCTTTGACGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
- - - - - ctgtatg
- - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctactg