Sequence
atgc intronic sequence ATGC exonic sequencegttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
Basic information
species | Glycine max |
transcript | GLYMA17G17450.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaa-aatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
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--------------------------------------taaactaacataaaatttatt-aatgtggaaaatcaagaatttcctagtttgtttcataacttactcttgact---gttctt---tgtacttctgcttggcattcagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
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----------------------------------------------------gtaagcttccaaagaactggtgaaagcaatctgtc-gccatgcatgcttgcttgatctgctgctgctgc-tgcttgtgttgtggatc--cagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118919_T01 (Zea mays), 3'ss of exon 3
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
||||||| ||| | | | | |||| | | | ||||| || | | | | ||| | || | || |||| | |||| | |||| ||| | || ||||| || || ||||| || || || || || | |||||||||||||| ||||||||||||||||| || || | || || || || || | ||| || |
-gtaaaaaaaaaaacctcacgctgctgcgttcatct----gtaggtgactgattccagtctgaat-ctgaaataatagacattgactggagcccgtaaaca-----aactcataaa-----atgtgcttg--tcgattcatcagGGAGCGCGCCCCTGACTGCGGTGCAGCTGCTCTGGGTGAACATGATCATGGACACGCTGGGAGCTCTGGCGTTGGCCACGGAGCCCCCCAACGACGAGCT
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataaga--aaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
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-----------------------------------------------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaatcattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
tcttc CT-rich tract
attttacatgtatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA