Sequence
atgc intronic sequence ATGC exonic sequencegtataaatttctgtacttggaatgctttggattgttgtcaccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
Basic information
species | Glycine max |
transcript | GLYMA19G29100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 4
------------------------gtataaatttctgtact-tggaatgcttt-ggattgttgtcaccagtacaaagt-------gattatataggatgaca-atttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
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gtagttattttctgcttcagtaaacagtggtttcctattttgttcagtgcttttgtgctgatgacattctgaccatatttcttcaggctttgcttaataaaatatttcttaccttttccccttttagTTGCAATGGAAGTCTTCAGTTGGGGAAGTGGGACAAATTATCAGCTGGGAACAGGCAATGCCCACATACAAAAACTACCATGCAAAGTAGATGCCTTGCA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G135133_T01 (Zea mays), 3'ss of exon 3
gtataaatttctgtacttggaatgctttggattgttgtcaccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
|| ||||| | | | | || | | | | | ||| | | || | || || ||||| |||||| || || || ||||| |||||||| ||||| ||||||||||||||||||||||| || | || || || || ||||||| ||||| || | |
--gtagctttcttctgccccaggaaatggttctcttatatcgcgctcttggcaatt---tggcttgctttatggaagtttttttcat-tttagTTGCAACGGAAGTCTTCAGTTGGGGAAGTGGGACAAATTATCAGCTTGGAACTGGCAACGTCCACATACAAAAACTACCATGCAAAGTAGAAGCTTTGCA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G893355_T02 (Zea mays), 3'ss of exon 5
gta-taaatttctgtacttggaatgctttggattgttgtcaccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
||| ||||| | |||| || || || | | | | | ||| | | || | || || |||||| || || || ||||| |||||||| ||||| |||||||||||||| |||||||| || | || || || || ||||||| ||||| || | |
gtagctttcttctgccccaggaaatggttctcttcttatatcgcgctcttggcaatttggcttgct--ttatggaaggttttttttcattttagTTGCAACGGAAGTCTTCAGTTGGGGAAGTGGGACAAATTATCAGCTGGGAACTGGCAACGTCCACATACAAAAACTACCATGCAAAGTAGAAGCTTTGCA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 4
gta-taaatttctgtacttggaat--gctttggattgttgtcaccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
||| ||||| | |||| | | | | ||| | ||| || | | ||| | ||| || ||||| |||||| || || || ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || || || ||||||| ||||| || | |
gtagctttcttctgccccaggaaacggttctcttatattgcgctcttggcaatttggct-tgctttatggaagttt----tttttttcat-tttagTTGCAACGGAAGTCTTCAGTTGGGGAAGTGGGACAAATTATCAGCTGGGAACTGGCAACGCCCACATACAAAAACTACCATGCAAAGTAGAAGCTTTGCA
upper sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0032g00280.t01 (Vitis vinifera), 3'ss of exon 4
gtataaatttctgtacttggaatgctttggattgttgtcaccagtacaaagtgattatataggatgaca-atttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
|| || ||||| | | | || | ||| | ||| | | |||| || ||||| || | | |||||| ||||| ||| | ||||||||||| |||||| || ||||| ||||||||||| || | || || || ||| ||||||| ||||||||||||||
---gtggttattgcacttgtcaatttattgaatcatgtggttgttggaaa----tctttagggataacctgagtgacttttcatgtctgtttagTTGCCACGGAGTTATTTAGTTGGGGAAGTGGTGTGAACTATCAACTTGGAACTGGGAACACTCACATACAAAAGCTACCATGCAAAGTTGATTCACTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
atttgac putative branch site (score: 4)
ttcatcttt putative PPT
aaagtgattatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaatttctgtacttggaatgctttggattgttgtcaccagtacaaagtgattatataggatgacaatttgactcttggttcatctttagTGGCCACTGAGGTCTTTAGTTGGGGCAGTGGTACAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGTAAAGTTGATTCACTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT