Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagtgtgtattttgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
Basic information
species | Glycine max |
transcript | GLYMA19G32010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G047310_T02 (Zea mays), 3'ss of exon 6
gtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagtgtgtattttgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
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-----------------------------------gtgagggatatacgatat----ttggattggcaatttttccgtctgcctatttttttgtctctatttttat---ggtcttttttatgccagATGATGGGAAACTACAAGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACTGTGAGTGATGATGATGT
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G180988_T01 (Zea mays), 3'ss of exon 6
gtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagtgtgtattttgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
||| || || | ||| || || | || || |||| || | | | |||| | | | || |||||||||| || | | | ||||||||||| |||||||| ||||| || ||||| |||||||| || |||||||| || | ||||| |||||| |
-----------------------------------gtgagggatatataatat----ttggattggcaatttggtcgtctggctttt---ttctctatctctattcttatggggtttttatgccagATGATGGGAAATTACAGGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACCGTGAGTGATGATGATGT
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagt---gtgtattttgatttgtttgtgactataaaaaggtgtcccac-attgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
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gtaag--ccaattgcac---cttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatac-----tttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtaagg-gcaaaaggcacatgttttcccatcacttg---atgaaaagcct--accatgtgattttgaatatatgatctccaagtgtgtattt----tgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
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gtaagagcacatgcattaataacttgctgatgttagcttcgcttttagtacttatgtattcaatctctgaacagagctcatttgcattttcattcttaacatttgtaattgctactcttcattcattaacgtaaat-gatgtttgcaatgccagATGATGGAAAGCTGGTTGCTGAGTCTGACTCAGGTGAATTCTGGGTCCTGTTTGGTGGTTTTGCTCCCATTGGCAAAAAGGTTGCCACCGAAGATGATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaagtgtgtattttgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
ttttgat putative branch site (score: 4)
tattttgatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcaaaaggcacatgttttcccatcacttgatgaaaagcctaccatgtgattttgaatatatgatctccaagtgtgtattttgatttgtttgtgactataaaaaggtgtcccacattgcagATGATGGCAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG