Sequence
atgc intronic sequence ATGC exonic sequence...aagaaatacttttactcgtttatcatattagtcaatattcaagaaataggaagggatgttatgcaacacagttttctaatgtcatttttatttgaaacagACCCTCGGTTGACAGATTATGATACCCTGCTCGAAAATATACAGGGTCTTAAAGCAGGGAAGCCTGTTCAAGTTCCAATATACGATTTCAAGTCTAGTTC
Basic information
species | Glycine max |
transcript | GLYMA05G07610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 2
aagaaatacttttactcgtttatcatattagtcaatattcaagaaataggaagggatgttatgcaacacagttttctaatgtcattttt---atttgaaacagACCCTCGGTTGACAGATTATGATACCCTGCTCGAAAATATACAGGGTCTTAAAGCAGGGAAGCCTGTTCAAGTTCCAATATACGATTTCAAGTCTAGTTC
| || | | | | ||| || | | |||| || | | | | | | | | | || || | ||| | | | | |||| || || ||||||| ||||| || ||||| ||||||||||| ||||| || | ||| | | | ||||| ||||||||||| ||||||||||| || |
-gttagta-tcagagtgctctattattacaaactgcattctctaaggttataatgtt-tcctaccagagaaattgatattttcacctcttaaaacttgcccagATCCACGTCTGACAGACTATGACACACTGCTGGAAAATATACATGGTCTGAAGGAAGGAAGGTCAGTTCAGGTTCCAATATATGATTTCAAGTCAAGCTG
upper sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 1
---aagaaatacttttactcgtttatcatattagtcaatattcaagaaataggaagggatgtta-tgcaacacagttttctaatg-tcatttttatttgaaacagACCCTCGGTTGACAGATTATGATACCCTGCTCGAAAATATACAGGGTCTTAAAGCAGGGAAGCCTGTTCAAGTTCCAATATACGATTTCAAGTCTAGTTC
|||| | ||| ||| | | ||||| | | | || | ||| || | |||| | | |||||||| | || ||||| |||||||| || ||||||||||||| || |||| || ||||| || ||| | |||||||||||||| ||||||||||| || |||||||| || ||||| ||
tcatagaagtgtatttttctctttgt--ttctagtccaaac---aatgattgaaagatgtgagactgcatggctgaattctaatggttgttacattttgagacagACCCACGCTTGACAGATTATGGCACATTGCTTGAGAATATCCATGGTTTAAAAGCAGGGAAGCCCGTTCAAGTTCCTATTTACGATTTTAAATCTAGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataggaagggatgttatgcaacacagttttctaatgtcatttttatttgaaacagACCCTCGGTTGACAGATTATGATACCCTGCTCGAAAATATACAGGGTCTTAAAGCAGGGAAGCCTGTTCAAGTTCCAATATACGATTTCAAGTCTAGTTC
ttctaat putative branch site (score: 2)
tttttattt putative PPT
ttttctaatgtcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaatacttttactcgtttatcatattagtcaatattcaagaaataggaagggatgttatgcaacacagttttctaatgtcatttttatttgaaacagACCCTCGGTTGACAGATTATGATACCCTGCTCGAAAATATACAGGGTCTTAAAGCAGGGAAGCCTGTTCAAGTTCCAATATACGATTTCAAGTCTAGTTC
aagaaata
- gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - ggaaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaca