Sequence
atgc intronic sequence ATGC exonic sequence...tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagctaacacatcctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
Basic information
species | Glycine max |
transcript | GLYMA16G26360.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 5
-----tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagctaacacatcctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
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tttattacacttgcctgtcccacaaggacagtaag--tcatttttttctgctaatg-ctggagaatattcttattttattttac--actggccacatttttgcagTATATTATCTTTCGTCGGGGCATTGGAATTGACCGTACAACCGATTACTTTATCATGGAGAAACTGGATGTGATCATATCCCGAGCTTGGAGCTCATTGC
upper sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g32490.1 (Oryza sativa), 3'ss of exon 5
tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagctaacacatc--ctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
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gatacctcatgatgatggcatacatttgatgataaatgcattttt--ttcagttctacataatatattgcataactaattatcacatcaaccatgcttgcagTACATTATATTTCGGCGGGGCATTGGAATCGACCGGACAACTGATTACTTCTTCATGGAGAAAGTGGATGTAATAATATCACGGGTGTGGAGATCATTGC
upper sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G011136_T03 (Zea mays), 3'ss of exon 5
-----------------------------------------------------tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtc--tgttcgtgaagtggcaagctaacacatcctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
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gtattattcgttcatgcaacttttcttttcatcctgatgatacttatgtttatgagggatgattagaaatctacaatagcattggatgttttcatcatcctctgttttttctcatggtttcctaagacacattcttcattgtccacatcttgtagTATATCATCTTTCGTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGC
upper sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 5
--tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagctaacacatcc--tgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
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aatttgtttgcttgttctaattttgtcttcacaagtattatttcctcggt---attttattatagttttca-gcagttatttcacgtcaccaacatctttacagTATATTATCTTCCGTCGGGGCATTGGGATTGATCGGACAACTGACTACTTCTTCATGGAGAAAGTGGATGTCATCATATCCCGAGCATGGAGGTCATTGC
upper sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
-tg-gacctgcatagattg-agacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagcta-acacatcctgttatttt-agTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT-
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atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctc--tcccaaaaag---aagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTA-ATGCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactcgattttagtctgttcgtgaagtggcaagctaacacatcctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
agctaac putative branch site (score: 2)
tcctgtt putative PPT
tgttatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggacctgcatagattgagacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagctaacacatcctgttattttagTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- -acctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacat