Sequence
atgc intronic sequence ATGC exonic sequence...taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
Basic information
species | Glycine max |
transcript | GLYMA20G34160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
----------------------------taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
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gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcat-gttcattttgaagaaatttt-ttaaataaactgcaatttgtgttgt---ttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacat-tgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
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-----------------gtatgatggt-ttgaattgattctgttttgcttgcattcgg--atgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
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-----------------------------------------gtacgtttgcggtgtttgtacgtgattcggtcgctctaacccggatttg----atgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
cattaac putative branch site (score: 2)
atcaagaaataaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacattgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa