Sequence
atgc intronic sequence ATGC exonic sequencegtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
Basic information
species | Glycine max |
transcript | GLYMA08G40980.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 3'ss of exon 9
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
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---------------------gtatgctaccttaagacatctatgcatgtatatcagctgcatgctgattgtctcttact--gttttggaatttgtagattgatggtgttcatccatatcgtttgctt---------tgcagTTGTCGTGGTTTCCCTTTTTCCTTTTTGATACTGACTGGATGGGACGTGAGGTTTACCATGGGGACCCAAATGGCAACTTGAGTGAAAGGAAAGCTTATG
upper sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgt-tgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
| | | || || | | | || | | | | || |||| | || || | | | || | ||||| | | | | |||||||||| ||||||||||| || || ||||| || || |||||||| | |||||||| ||||| |||||||| || || ||| | |||||
----------------------------------------gtacgctaccagattacatatatacatgcctaccgactccttgctgatggtttgttttattcgaggt--tgatgatttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
upper sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcc-tagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
|| || | | | || | || | || || | | |||| | | || | || | || ||| | | | || ||| || || || | || | | || | | ||||||| || ||||| |||||||||||||| ||||| ||||||||||| ||||||||||| ||||| ||||||| ||| || | || | | || || ||||
gtgagtgccaaagaaaaattatga-----tcagttattacatat---ttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgat------tgtggtcttgttc-tttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
upper sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32955 (Selaginella moellendorffii), 3'ss of exon 9
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
|| || || | ||||| | | | ||| | | ||| | || |||||||| ||||| || |||||||||||||||||||| |||||||||| | |||||||| || | | | | | | |||
----------------------------------------------------------------------------------------gtaagaatctctt----ttcttctagt-tgatttctaactttgtggtttctcagCTATCCTGGTTTCCTTTCTTCCTCTTTGATACGGATTGGATGGGCCGAGAAGTTTACAACGGTGATCCTTCTGGTGGTATTGACAAGGCGAAGAGCTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
ctttaat putative branch site (score: 4)
tcctatct CT-rich tract
ttttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcctagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG