Sequence
atgc intronic sequence ATGC exonic sequence...cgagaaaagaagccgctcagtttctttttttcattttcagtacacgcatgtctaacatacatatgcacgcacaccgtttatcacgtttaattcgatgcagCTCGTTTTGGAATCGACGGCCATCATCGTCTGCCTCAACGGAGAATACCGTCCAACTCGCGTGTTCCCGGAGCTGTCCTCCAAGTTGCTTGACTTCTTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g44134.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g44134.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004752_T01 (Zea mays), 3'ss of exon 3
--------------------------------cgagaaaagaagccgctca-gtttctttttttcattttcagtacacgcatgtctaacata---catatgcacgcac-accgtttatcacgttta---attcgatgcagCTCGTTTTGGAATCGACGGCCATCATCGTCTGCCTCAACGGAGAATACCGTCCAACTCGCGTGTTCCCGGAGCTGTCCTCCAAGTTGCTTGACTTCTTCT---
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gtacgtctcggcggcatctatactttggtgaccggcagtggcggccacagacagttcgcacacacatgtacacggtacacctctcgatctcctctcgtgtgagctgatgagtgatgaccatgattatatgcctatggcagCTCGTGCTAGAAGCGACGGCCACTGTCGTCTGCCTCAACCAAGAGTACCGCCCAACTCGCATGTTCCCGGAGATGGCC---AAGCTGCTGCCCTTCTTCTCTC
upper sequence: LOC_Os02g44134.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G306566_T01 (Zea mays), 3'ss of exon 3
-------------------cgagaaaagaagccgctcagt--ttctttttttcattttcagta----cacgcatgtctaaca-tacatatgcacgcacaccgttta----tcacgtttaattcg-atgcagCTCGTTTTGGAATCGACGGCCATCATCGTCTGCCTCAACGGAGAATACCGTCCAACTCGCGTGTTCCCGGAGCTGTCCTCCAAGTTGCTTGACTTCTTCT
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gtatgcgcgtgcacgtgcacgtgtaaataaatcaaaggatcatcctcacatgaaccggccatggcggcacgtgagccgagcgctactatttcacacgcaccgcctgatctttaggctcggccggcatgcagCTCGTCCTGGAAGCGACGGCCACCGTGGTCTTCCTCGACAAAGACTACCGTCCGACGCGCGTGTTCCCGGAGGTGGCGTCCAAGATGCGGCTGCACTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgtctaacatacatatgcacgcacaccgtttatcacgtttaattcgatgcagCTCGTTTTGGAATCGACGGCCATCATCGTCTGCCTCAACGGAGAATACCGTCCAACTCGCGTGTTCCCGGAGCTGTCCTCCAAGTTGCTTGACTTCTTCT
tttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagaaaagaagccgctcagtttctttttttcattttcagtacacgcatgtctaacatacatatgcacgcacaccgtttatcacgtttaattcgatgcagCTCGTTTTGGAATCGACGGCCATCATCGTCTGCCTCAACGGAGAATACCGTCCAACTCGCGTGTTCCCGGAGCTGTCCTCCAAGTTGCTTGACTTCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - aaaagaa
- - - - - -gccgctc
- - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacgc