Sequence
atgc intronic sequence ATGC exonic sequence...ccaacctaccaaccaaaacagaagcatgcacgtgcatatgttgaaagcatacgatgattttatgaaacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT
Basic information
species | Glycine max |
transcript | GLYMA20G38420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------ccaacctaccaaccaaaaca------gaagcatgcacgtgcat-atgttgaaagcatacgatgattttatgaaacatgaatataatacgtatggatacgtgctt-cagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT---
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gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagattatattgttgttgttctattctatcatttcatgtggtctgaaaaagcacac-cacatgcatgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAG--GACCGCGAGGAGCGGAAGGTGGAGGC-GGAGACGATGGCGCGGATCGA
upper sequence: GLYMA20G38420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------ccaacctaccaaccaaaacagaagca-tgcacgtgcatatgttgaaagca--tacgatgat-tttatgaaacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT-----
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gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtatcgatctcattgacctcttcttggcattattatactatacatgc-tgc-tatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGT-----ATCTGGGACAAGAGTCGGCGCTGCAGAAGAATCCATCCGATGGACA
upper sequence: GLYMA20G38420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
ccaacctaccaaccaaaacagaagcatgcacgtg-catatgttgaaagcatacg-atgattttatga-aacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT
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-aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatg--acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcatacgatgattttatgaaacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT
atgattttatgaaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaacctaccaaccaaaacagaagcatgcacgtgcatatgttgaaagcatacgatgattttatgaaacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
ccaacct
- - - - ccaacca
- - - - - - - -aaacagaa
- - - - - - - - - - - - catgcac
- - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - gcatacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat