Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagcacttaatagattactgctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
Basic information
species | Glycine max |
transcript | GLYMA11G12270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G12270.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g04030.3 (Oryza sativa), 3'ss of exon 4
----------------------------gtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagcacttaatag-------attactg----ctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
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gtaatccaatccatccacaatcttttcgatgtcaatgtcacatcgatcattcgtaattaagctacatttgatcaatttgcaactaaacattacataatgtttgcatttatgtgccctgttttaaccagGTCCTAGGCAACAAGTACCAGAGCAAGCTGCTGGAAGTGATTGATCCCAG
upper sequence: GLYMA11G12270.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagcacttaatagattactgctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
| ||| || | | ||||| | || || | | | | || || |||| || | || ||| | ||||| || || ||||| ||||| ||||||||||||||||| |||||||| ||
gcaagtata---caaaccctttttatcac----tcttgactgatataaatgag-agatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
upper sequence: GLYMA11G12270.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g04480.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagc-acttaatagatta-ctgctttattg-accagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
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gtgaccatt---tgtcttctgtttaccttaaactattacttgttttgatcaaacaaaatccacttaaccatctaacggttttattgtaccagGTGTTGGGTAATAAATACCAGAGCAAGTTGCTTGAAGTAATCGATGCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgtacgtttcagttaagtaggagcacttaatagattactgctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
acttaat putative branch site (score: 4)
ctgcttt putative PPT
ttaatagatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagcacttaatagattactgctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG