Sequence
atgc intronic sequence ATGC exonic sequence...gtctaatagtggagctaatccatgggttcagtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
Basic information
species | Glycine max |
transcript | GLYMA08G13810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 6
-gtctaatagtggagctaatccatgggttcagtttgggtcattatattaacaggacttgtcaaattaacata-tatgtgtgttttcc-ccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
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cattttattgacatttggactcttcaccttgaaatga--cattaaaaggagaaaaac-atgaatttgatgtaatttactaaccttctactagcgcaaatgcagATCTTCTTCCATCCCGAGATTTACTCTGCCGACTTCTCCACTCCTCTACCTGAACTAATTGATAGCTGTGTTCAATCTGCGCCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 5
-gtctaatagtggagctaatccatgggttca-gtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
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taacttgcttgggactaaaagactatgttgatgtacagttggtcatgttttttaggtcag--aattaggtgtgcatctctaatcatttaccaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G305332_T01 (Zea mays), 3'ss of exon 1
-gtctaatagtggagctaatccatgggttcagtttgggtcattatattaac-aggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
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tttgttagaataaacttttaacttgttttcagtt--ggtcatgattttttttaagaagtcagaatttggtgtgcgtctctaatcatctagcaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGACTTCTCCACTCCTTTACCTGAGTTGATTGATAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
gtctaatagtggagctaatccatgggtt-cagtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctg---cagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
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---caagagagtaactggaaagtggaacataatttcctttattgttcttgc-gtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 5
------gtctaatagtggagctaatccatgggttca-gtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
| | || | | ||| | | | | | || | | | | | |||| | | |||| | | || || | || ||||||||||||| ||||| ||||| || |||| || ||| | |||||||| |||| ||||||||||||||||||||||||||| |||||||||||||| ||
tgtttacttgtgcattgcatttcatctactagatgatgctttgataagtcttttaaaaaaag-----gaatt--tgtttttgatgattaatctggctgattatgcagATTTTCTTCAATCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
tttctgc CT-rich tract
tcaaattaacatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaatagtggagctaatccatgggttcagtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctgcagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - tccatgg
- - - - - - - - - - - - - - - gtttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtca