Sequence
atgc intronic sequence ATGC exonic sequencegtaagacttcatgcatcattgctcccattctttccattgttacgtgtctttatgttctatgattagaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
Basic information
species | Glycine max |
transcript | GLYMA20G30340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30340.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g53520.1 (Oryza sativa), 3'ss of exon 4
gtaagacttcatgcatcattgctcccattctttccattgttacgtgt-ctttatgttctatgattagaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
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---------------------------------gtaatgataccagtgctgcgaagcttaagtttggcaaactat-ttgatacaagttta-taacaacctttttttggggctgaatgcagTTTTTGTGGCGCTCTACACTGTGCCAGTACTGTATGAGAAGTATGAGGACAAGGTTGATGCTTTTGGTGAGAAGGCTGAGATTGAATTTAAGAAGTACTA
upper sequence: GLYMA20G30340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G031308_T02 (Zea mays), 3'ss of exon 4
gtaagacttcatgcatcattgctcccattctttccattgttacgtgtctttatgttctatgattagaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
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--------------gtaatgaccgcaattcatctgctactaactttttctcttggtgt-tgattcaagttttg----aatgaagtttta-------tgcctccattt---------cagTCTTTGTGGCACTGTACACTGTACCAGTTCTGTATGAGAAATATGAGGACAAGGTTGATGCTTTTGGTGAGAAGGCTATGACTGAACTGAAGAAGTATTA
upper sequence: GLYMA20G30340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G002786_T01 (Zea mays), 3'ss of exon 4
gtaagacttcatgcatcattgctcccattctttccattgttacgtgtctttatgttctatgattagaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
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--------------gtaataactgtgattcat-ctgttgctaacttttctcttggtgt-tgattcaagttttg----aatgaaatttta-------tgcctccatt---------gcagTCTTTGTGGCACTGTACACTATACCTGTTCTGTATGAGAAATATGAGGACAAGGTTGATGCTTTTGGTGAGAAGGCTATGATCGAACTGAAGAAGTATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
tcctaac putative branch site (score: 1)
tatattaatggtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacttcatgcatcattgctcccattctttccattgttacgtgtctttatgttctatgattagaaggctatattaatggtattttcctaacactgaatccatttgggatgatacagTCTTTGTGTCACTGTTCACATTGCCACTGCTGTATGAGAAATATGAAGACCAGGTTGATGCATTAGGTGAGAAGGCAATGATTGAGATCAAAAAGCAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA