Sequence
atgc intronic sequence ATGC exonic sequence...agtgcagattttcaagaatgttaagtgagaatgagatctgagggacaatgaaatgggttgaaaacgtagtttttaactgtttgaacatgctttcatgtagGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
Basic information
species | Glycine max |
transcript | GLYMA09G17040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 2
--agtgcagattttcaagaatgttaagtgagaatgagatctgagggacaatgaaatgggttgaaaacgtagtttttaactgtttgaacatgctttcatgtagGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
| | | | | || | | | ||| ||| | | || | | ||| | | | | || | ||| | | || | || |||||| |||||||| |||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| ||||| ||| | || | || || ||
aaggagaataatgtctata-tagtaattgatcttaaaatgttcagcttaatttt-tattctcactgcatattcacattatgtgtttatttgttgatattcagGTATCGTTCTGGACTCTGGTGATGGTGTGAGCCACACAGTCCCCATTTATGAAGGGTATGCCCTCCCACATGCCATCCTGCGTCTTGACTTGGCAGGACG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------------------agtgcagattttcaagaatgttaa--gtgagaatgagatctgagggacaatgaaatgggttgaaaacgtagtttttaactgtttgaacatgctttcatgt-agGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
||| ||||| || | | |||| | | | | | | || | | ||| ||| | || ||| | |||||||||||| || || ||||| ||||||| ||||| ||||||||||| |||||||| | ||||| ||||||||||| | |||| ||||| || ||
gtatggagttttttttttcctttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttgtgatcagGTATTGTTCTCGACTCGGGTGACGGTGTCACGCACACTGTTCCAATCTACGAAGGCTACTCACTGCCCCATGCAATCCTCAGGCTGGACCTTGCCGGTCG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------agtgcagattttcaa-gaatgttaagtgagaatgagatctg----agggacaatg----aaatgggttgaaaacgtagtttt-----taac----tgtttgaacatgctttcatgt-agGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
|| |||| | | | |||| | | || || | ||| || | |||| | | |||| |||| ||| ||| | || ||| | |||||||||||| || || ||||| ||||||| ||||| ||||||||||| |||||||| | ||||| ||||||||||| | |||| ||||| || ||
gtatggagtttttttatcccttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttgtgatcagGTATTGTTCTCGACTCGGGTGACGGTGTCACGCACACTGTTCCAATCTACGAAGGCTACTCACTGCCCCATGCAATCCTCAGGCTGGACCTTGCCGGTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgaaatgggttgaaaacgtagtttttaactgtttgaacatgctttcatgtagGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
ttttaac putative branch site (score: 2)
tgctttc putative PPT
tagtttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgcagattttcaagaatgttaagtgagaatgagatctgagggacaatgaaatgggttgaaaacgtagtttttaactgtttgaacatgctttcatgtagGTATTGTTCTGGATTCTGGTGATGGTGTCAGCCACACAGTTCCAATCTATGAAGGCTATGCCCTGCCACATGCAATCCTTCGTTTGGATCTTGCGGGGCG
- - - - - - - - - - - - - - gaatgag
- - - - - - - - - - - - - - - - - - - tgaggga
- - - - - - - - - - - - - - - - - - - - - - -caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatgc