Sequence
atgc intronic sequence ATGC exonic sequencegtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatttgcattagccaaagtttttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
Basic information
species | Glycine max |
transcript | GLYMA02G05420.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------gtttttcctcatg--ataatcggataatatatatt------taaaatttaaagtaaatttgcattagccaaagttttta----------cttcctttaaattaa-----aaactatgttctctttatttctca-ggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
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gttacaatgccatttttcttttggtttgatatggtttagcttactcatattttgtcttatgcaatatgcagtttgtatgttttagcagctaagccttgacaataaaatatattatatgaagaccatatagtgttgagctttcctcacattagttttgagagcagctgacctgtgttttagGTGGTGTTGTTGCATCTGCTGCATATAAAAAATGGGAGAGAGCTGCCATGGCTGGTGTTTCTTTGGTTGCTGATGCAGCTGAAGAGCTTGAGCGCAACAC------------------------------------------------------------------
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
---------------------gtttttcctcatgataatcggataatatatatttaaaatttaaagta-aatttgcattagccaaagttt--ttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctg--cttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGA-GCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGA--AGTTTTATCCT-----
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gtgggcgcatgttctctgttagtctgttcttttgtta--tgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaaactat---caaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtg-gatagatggtgacctgt--gttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATG--GGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 7
---------------gtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatttgcattagccaaagtttttac----ttcctttaaattaaaaactatgttctctttatttctca--ggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
||| | | | || | | | ||| | || |||| || | | | |||||| || ||| ||||| | |||| | | ||| || | | | | || | || || || | | ||| | | | | ||| ||| | || | | |||| |||| || | | | | || | | | | | | | |||| | | |
gtgggcacatattctctttccctttgttatgacctagccttgcctatct-----tttgtcaaaatctgtgt-ggttagagttttggtgaaattgtttttgattaattatcatgtagaggaccctctctagtggtgaatctttgttgcattaatgtggatagctggtgagctatgttttagGTGGCGCTGTTGCATCTGC---TGCATATAAGAAATGGGAGAGAGCAGCCATGGCTGGTGT--TTCTTTAGTTGCTGATGCAGCTGAGGAGCTCGAGCGCAACAC----------
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G36960.2 (Arabidopsis thaliana), 3'ss of exon 7
gtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatttgcattagccaaagtttttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
| | |||| | || | | | ||| || | || |||| || | | | ||| |||| | | || | |||||| ||| |||| | | ||||||||||||||| || |||||||| | ||| || ||| | ||||| |||||||| ||||||||||| ||| | ||| || |||| || || |
-taatcttccatgttgatattagattttatgttgctatttaaaagc---ttgatgtagttccaggttcttacgtgactctaagca----------tctcttcctttttcag---------------cagGTTATAGAAAATGGGAAAAAGCTGCAATAGATGGGGTCTCTCTGGTTGCTGATGCTGCAGAGCATTTGGAACGAACATCAATTGACAAAGATATGGATGA---------------------------------------------
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 7
--gtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatttgcattagccaaagtttttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
| | |||| | || | | | ||| || | || |||| || | | | ||| |||| | | || | |||||| ||| |||| | | ||||||||||||||| || |||||||| | ||| || ||| | ||||| |||||||| ||||||||||| ||| | ||| || |||| || ||
ttttaatcttccatgttgatattagattttatgttgctatttaaaagc---ttgatgtagttccaggttcttacgtgactctaagca----------tctcttcctttttcag-
upper sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0040g01460.t01 (Vitis vinifera), 3'ss of exon 6
gtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatt-tgcattagccaaagtttttacttcctttaaattaaaaacta----tgttctcttt--atttct--caggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
| |||||| | | ||| || | | | | ||| | |||| | ||||| || |||| ||| |||||| ||| | | ||||| | ||||| |||| || |||||| || |||||||||||||| |||||| | ||||| |||||||| ||||||||||||||| | | |
-----------------tgaaataataaacgca-agttcttacgatatgccattccatggtcaag--tgccactttagtaaaattttggtctggtcttgttgattttggatttctagcagCTGCTGTTTCATCAGCTGCATATAAAAGATGGGAAAAAGCTGCAATTGCTGGGGTTTCTCTGGTTGCTGATGCTGCAGAGCATTTGGAGCGAACAACTAA--------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
tgtttcttt CT-rich tract
ttatagaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttcctcatgataatcggataatatatatttaaaatttaaagtaaatttgcattagccaaagtttttacttcctttaaattaaaaactatgttctctttatttctcaggtacgatttcaacggctgcttatagaaaatgggagaaggctgcaattgctggtgtttctttagTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAACTGTTAAAGGAATTGAACAAGACCAGGAGAATCCAGGTAGCTACCACACTTGAAGTTTTATCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG