Sequence
atgc intronic sequence ATGC exonic sequence...tttaaatttcaatactaaaaacttgtttatgaaggaggaactgggactatgcttaattttgtgttctatgtagttcattcccccttttttcatcaaacagGAAGACATCATTCGAAGATGTCAAATTATGCAAAAGCCTGTTATTGTGGCAACAAATATGCTTGAAAGCATGATTAATCATCCCACACCAACAAGGGCAG
Basic information
species | Glycine max |
transcript | GLYMA01G40860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------tttaaatttcaatactaaaaacttgtttatgaaggaggaactgggactatgcttaattttgtgttctatgtagttcattcccccttttttcatcaaacagGAAGACATCATTCGAAGATGTCAAATTATGCAAAAGCCTGTTATTGTGGCAACAAATATGCTTGAAAGCATGATTAATCATCCCACACCAACAAGGGCAG
| | | | | || |||| | | | | || | ||| | | || || | | || | | || | | | | ||||| |||| ||| || ||| || ||||| || ||| | || || |||||||| || ||||||||| | |||||||||||| | ||||| || ||||| |||||||
gtgagatcacattacatgtacagttttaggtgcaccaagtcatttcttactgtatctagtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataa-attgtgactgttttacttctctttttt--------cagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCCACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCAACTAGGGCAG
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 7
tttaaatttcaatactaaaaacttgtttatgaaggaggaactgggactatgcttaattttgtgttctatgtag-----ttcattcccccttttttcatcaaacagGAAGACATCATTCGAAGATGTCAAATTATGCAAAAGCCTGTTATTGTGGCAACAAATATGCTTGAAAGCATGATTAATCATCCCACACCAACAAGGGCAG
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-ttaaatggtgatc----agccttttcaatcagtgtgagttcatttcttttcctgattcccttttccaattaaacaaactaaatctcatgttaacttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCAACAAACATGTTGGAGAGCATGATTAATCATCCTACACCAACAAGGGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatgcttaattttgtgttctatgtagttcattcccccttttttcatcaaacagGAAGACATCATTCGAAGATGTCAAATTATGCAAAAGCCTGTTATTGTGGCAACAAATATGCTTGAAAGCATGATTAATCATCCCACACCAACAAGGGCAG
gcttaat putative branch site (score: 4)
ttcattcccccttttt putative PPT
ttaattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaatttcaatactaaaaacttgtttatgaaggaggaactgggactatgcttaattttgtgttctatgtagttcattcccccttttttcatcaaacagGAAGACATCATTCGAAGATGTCAAATTATGCAAAAGCCTGTTATTGTGGCAACAAATATGCTTGAAAGCATGATTAATCATCCCACACCAACAAGGGCAG
- - - - - - - -taaaaac
- - - - - - - - - - - - - - - - -ggaggaa
- - - - - - - - - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtag