Sequence
atgc intronic sequence ATGC exonic sequence...ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgatcattctaatttggttacacccttgattttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
Basic information
species | Glycine max |
transcript | GLYMA13G31830.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgatcattctaatttggttacacccttgattttgaat-ttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
| || | |||| || | ||| || ||| ||| | | |||| | | | ||||| || ||| | |||||||||||| ||||||||||| ||||||||||||||| |||||||| ||
-----------gttgtgaatatacttgtgtttttgttatttctgcacacta-tttcttcttatatttgacatagtgtattgttacaatgta--tgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
ttcaatcctgcacaatcaaacaaagtgtgcttgcata---ttttgatcattctaatttggttacacccttg-attttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
| | ||| | || || || | || | |||| | | || || | | | || || | | ||| || || || || | || ||| ||||| ||||||||||| ||||| |||||||| |||||||||||
gttggatatattaaat-gagcattgt-tggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcc--tgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 7
ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgat-cattctaatttggttacacccttgattttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
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--gttgtgtgtatgtttctgctgtgtctattcatgcacattgccacattgtaccctcctc---catttcacattatgtttatttaaatgtg--tattacagGACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT
upper sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 8
--ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgatcat--tctaatttggttacacccttgattttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
|| | | || || || ||| || | | | | || | | | || | || | ||| | || | || || ||||| ||| ||||||||||| ||||||||||||||| ||||||| ||
ccaccatccatatgtgtgtgtgcat-gtatgtttgtatgtgt-gtttatggttttacctgacaattttctgttatctgatcacactacaacat--ttcttacagGAATGAAAGTGCTTTGAAGTTTGGATGGTTTTTCATGTTTTATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctaatttggttacacccttgattttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
ttattttt CT-rich tract
ttgattttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgatcattctaatttggttacacccttgattttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
- - -tcctgca
- - - - - - - - -aaacaaa
- - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccctt