Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
Basic information
species | Glycine max |
transcript | GLYMA18G50270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G50270.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G123305_T01 (Zea mays), 3'ss of exon 4
gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
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--------------------------------------------------------ctagtttttccttataaacaacttgagacgttctggttcc-tgaataagttttcagaagagctttgtattttgatctttt------ctggatgttgaactttt------gcagGATATCTATTGTTTGAATGCTGATGGGTCTCTGTTTGATGCTGCACTTATTTCAGCAGTGGCTGCCTTTACACATT
upper sequence: GLYMA18G50270.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G886044_T02 (Zea mays), 3'ss of exon 3
gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttcttta---tcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
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-------------------------------------------------------------------ctaatttttcttta---taaacaagttgagatgttctggat--cctgaataagttttcataagagctttgtattttgatcttttctgggttttgaacttttgcagGATATCTATTGCTTGAATGCTGATGGGTCTCTGTTTGATGCTGCACTTATTTCAGCAGTGGCTGCCTTCACACATT
upper sequence: GLYMA18G50270.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G60080.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
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----------------------gtgagtactcgttggtcttatatcggtgcttgtccgtcagttgattcacatctattct----tctagggatctttctctttgata---tttaactgagttctctagcatatatatgaacattgt-tgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
upper sequence: GLYMA18G50270.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08550.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtac-actgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
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----------------------------------------------------------------------tagttggtgctctcagtgagtgactttagccaagtgtgaacatcgtgcatttttttgtttctgtattgaatgacaaagaaatacatttggtatctggcagGACATATACTGTTTGGATGCAGATGGTTCTCTGTTTGATGCTGCTTTACTTGCAGCAGTGGCTGCCTTCTCTCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
ctctgat putative branch site (score: 4)
ctgccttctttatc putative PPT
ttattatcaatctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC