Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcatgaaaaaatgcttcccttttgccaattttacttaattagtgtgtataacaactctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
Basic information
species | Glycine max |
transcript | GLYMA19G40050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 5
gtgagtcatgaaaaaatgcttcccttttgccaattttacttaattagtgtgtataacaactctatatttatgatggaaccaaccatt-------tgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
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gtgagtaatatatcgttaccactacggtgatgactttctgcccata-taaacataatgaagttaaattttctgtcgttccatcttctgtggacatatttagGAACTTGACTGGGAATCAATAGCTGCTGGTTTATTGCATGACACTGTTGAAGATACAGACATGGTTACTTTTGAAAGAATAGAAAATGAGTTTGGTGTAA
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 4
gtgagtcatgaaaaaatgcttcccttttgccaattttactta---attagtgtgtataaca-actctatatttatgatggaaccaacc---atttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
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-aatttgattgacaatcagtgacgctatggtgatgcaatctatgtacttgtccctactatacacagtgaatctaagttctactctgctttgatataattagGAACTTGACTGGGAATCCATCGCTGCTGGTTTATTGCATGACACTGTTGAAGATACGAATGTGGTTACTTTTGAAAGAATAGAAAATGAGTTTGGGCCAA
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G02260.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtcatgaaaaaatgcttcccttttgccaattttacttaattagtgtgtataacaactctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
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gtgagttgcgtg---atacgttgtgaatatggattc-acatgaggatta-gttggaaagcttaataattacttttg-------tacttgtatagGAATTGGATTGGGAGTCTATTGTTGCTGGATTACTACATGACACAGTCGAGGATACAAATTTCATTACTTTTGAAAAGATAGAAGAAGAGTTTGGTGCAA
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtcatgaaaaaatgcttcccttttgccaattt--tacttaattagtgtgtataacaact--ctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
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gtgagttatggaaattttgggaatatgttcttatttgtcacataatttattcttcctgcaattagcaatatagtttacttattgaatt-ttcatttagGAATTGGATTGGGAGTCCATTGCTGCTGGATTACTGCACGACACTGTTGAGGATACGAATGTTGTCACTTTTGACAGTTTAGAAAGGGAGTTTGGTGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattagtgtgtataacaactctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
gtataac putative branch site (score: 3)
tttgtct putative PPT
aactctatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcatgaaaaaatgcttcccttttgccaattttacttaattagtgtgtataacaactctatatttatgatggaaccaaccatttgtctagGAACTTGACTGGGAGTCGATTGCTGCTGGATTACTTCATGATACAGTTGAGGATACAAATGTTGTTACTTTTGAGAGGATAGAGGAGGAATTTGGTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA