Sequence
atgc intronic sequence ATGC exonic sequencegtgatttaataactgaaaacgtattttagaagttcttatttaaattgcatctaacgacaacctttttggcagcatctacgtgagatgagtataacaaatttgtcacatggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
Basic information
species | Glycine max |
transcript | GLYMA09G23250.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 3'ss of exon 9
gtgatttaataactgaaaacgtattttagaagttcttatttaaattgcatctaacgacaacct--ttttggcagcatctacgtgagat-gagtataacaaatttgtcacatggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
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gtaatctaagaataagttttctgttcta-aatctgatagtcttatcagattcatgtatgatctcgttctgatgatgctttatcatgattgagagtgacaaatat------tgcttatttt-------agttactg-acaggcagatgtgttatattactaacagGTCTTGGTTTCAGTATCGGAAACATGTTCCATGATTTTATACATCAGGGATGTTGACAAGCTTCTTCTGCAATCAGATAGATTTTACAAATTGTTCCGGA
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 3'ss of exon 8
gtgatttaataactgaaaacgtattttagaagttcttatttaaattgcatctaacgacaacctttttggcagcatctacgtgagatgagtataacaaatttgtcacatggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
|| || | || | | | || | ||| | | | | | | |||| | | || | | | | || || | | ||| | |||| || | ||||||| || |||| ||||||||| |||||||||| |||||||| ||||||||||| ||| ||||| || || | || |
--------------------------------------------------------gtaatctatgaggaatcggttttctgttctaagtctgagagtcctagct----atcacattcatgcttgatctt-gttttgatgatgt-gttatattactaacagGTCTTGGATTCAGTATCAGAAACATGTCCCATTATTTTATACCTCAGGGATGTCGAGAAGCTTCTTCTCCAATCAGAAAGATTATACAAATTGTTCCAGA
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 9
gtgattta--ataactgaaaacgtattttagaagttcttatttaaattgcatctaacgacaacct--ttttggcagcatctacgtgagatgagtataacaaatttgtcacatggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
|| || || || | | | || || | | | || || | | | || ||||| | | ||| | || | || || ||| || |||| | || || || || | | ||| | ||||||| | | ||| | ||||||| ||||||||||||||||||||||||||| | ||||||||||| || || || || || | || |
gtaatctaggatgaataagttttctgttctaaatctgagagtcctatcatattcatgcatgatctggttttgatgatgttttatcatgattgagagaagaggcaaatct--tgcttatttt-------agttactg-acaggcagatgtgttatattactaacagGTCTTGGTTTCAGTATCGGAAGCACGTTCCATTATTTTATACATCAGGGATGTTGAGAAGTTTCTTCTCCAATCAGATAGATTTTACAAATTGTTCCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
cactaac putative branch site (score: 1)
tttttgc putative PPT
atcattgtaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttaataactgaaaacgtattttagaagttcttatttaaattgcatctaacgacaacctttttggcagcatctacgtgagatgagtataacaaatttgtcacatggctatcttcaagtagagtttttacactaacaagatcattgtaatttttgcagCTTTTGGTTTTTATCACAGAAACTAGTTCCATCATTTTATACATCAGGGATGTTGAGAAGCTCGTTCTCCAATCACCAAGGTTATATAATTTACTACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC