Sequence
atgc intronic sequence ATGC exonic sequence...ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
Basic information
species | Glycine max |
transcript | GLYMA09G38730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 3
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgaca--taatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
| | | || ||| | |||| | || | || | | | | ||||| | || | | ||| | || | ||||||||||| || ||||| |||||||||||||||||||| || || || || || || ||||||||| |||| ||||| || || ||||| |||||
-agtcactaggaatcatt-acttagttgattattttataatcttttggtttcatttatttttagcctgcagttcagttatggttcaaattattattatgtagATTAGACACGGAGAAGCCGTTGGAATAATTGGTCCTTCGGGAACAGGAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
-----ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
|||| | || | | |||| | || || ||| |||| | ||| | || ||| ||| | || | | | | || |||||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| || | |||||| |||| ||||| || ||||||||||||||
actacgcattctgttcactgttatattttgat--gttttcatgactcagtag--gtttggt-ttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
|||| | || | | |||| | || || ||| |||| | ||| | || ||| ||| | || | | | | || |||||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| || | |||||| |||| ||||| || ||||||||||||||
gcattctgttcactgttatattttgat--gttttcatgactcagtag--gtttggt-ttgttgtagttatgattcaaaataatgttatacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
--ccattattttgataaattcatttaggcaggtcttgctgattcagcaat---tgttaaatctttttgctgttttttttt-ttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
|| || || | | | | | | ||| |||| | || || | | |||| | | | ||||||||||||||||||||||||| | |||||||||||||| || || ||||| ||| |||| |||||||| ||||| ||||||||||| |||||
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 2
-ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
||||| | | ||| | | | || | | |||| | || | | | | ||| ||| || | | || | | | |||||||||||||| ||||||||||| || ||||| |||||||| || || ||||| |||||| ||||||||||||| |||||||||||||| |||||
gagtggatttttttgtctctcttttcatatttagtttcccttgaattttggttatgttttatcattctctgtttattttcttactttaacccattta-tagATTAGACATGGGGAAGCTGTTGGGATTATTGGGCCTTCTGGCACTGGGAAATCAACAGTTCTGAAGATTATTGCGGGACTTCTTGCTCCAGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ22908 (Selaginella moellendorffii), 3'ss of exon 1
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
|| |||| |||| ||| | | || | | | || | |||| || || | | |||||||| ||||| ||||| ||||| |||||||| || || || || || ||||||||||||| ||||||||||||| ||| |||||
--------------------------------gtgtggattgagcagca--taacgactgtcactctctaaatccttttctttt---------tgtgcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ30431 (Selaginella moellendorffii), 3'ss of exon 1
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
|| |||| |||| || || | || | | | || | |||| || || | | |||||||| ||||| ||||| ||||| |||||||| || || || || || ||||||||||||| ||||||||||||| ||| |||||
--------------------------------gtgtggattgagcagca--tagcgattgtcactctctaaatccttttctttt---------tgtgcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
ttctgac putative branch site (score: 2)
tctttttgctgttttt CT-rich tract
ttaaatctttttgctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - -gcaggtc
- - - - - - - - - - - - - - - - -tgctgat