Sequence
atgc intronic sequence ATGC exonic sequence...gtttagggccattacaaggcaattgaaatcaaagaatccaaatatatttatccagataagcaaagcaacctgttgagaaagccttctctgtttaatgcagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G821024_T02 (Zea mays), 3'ss of exon 3
---------------------gtttagggccattacaag----gcaattgaaatcaaagaatccaaatatat-ttatccagataagca-----------aagcaacctgttgagaaagccttctctgtttaatg---cagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
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gttatctcctgtcctgaccaactttattctcttgaaaaatactgtagttatcttctgagcagataggtagatattagttggactagcctatcatttatcaagcaatttgttga-aaccctggttgtgtttgatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAGGGCAGGTCCCTAACATAAACGGGAATCCCTTCAACGGAGGACTACCCCA
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G079365_T01 (Zea mays), 3'ss of exon 3
gtttagggccattacaaggcaattgaaatcaaagaatccaaatatat-ttatccagataagca----aagcaacctgttgagaaagccttctctgt---ttaatgcagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
| || || || || || || | | | || ||| | |||| ||||| ||| | | || || | ||| || |||||||||| ||||| ||| | | |||||||| ||||||||||||||||| ||||| || || || ||||||||||| || |||||||||||||||| ||
--------ctcctaaaaaacagttatcttctgagcagatatgcagatattagttgaacaagcgtatcaagcacccttgttaataaaccctggttgtgttttgatgcagCTCTAAATGATGCCTTGAGGGAAGAAGTCCAGCGGCTTAAGATAGCCGCAGGGCAGGTCCCCAACATGAACGGGAATCCCTTCAATGGAGGACTATCACA
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G821024_T01 (Zea mays), 3'ss of exon 3
gtttagggccattacaaggcaattgaaatcaaagaatccaaatatatttatccag-ataagcaaagcaacctgttgagaaagccttctctgtttaatg---cagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
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---tactgtagttatcttctgagcagataggtagatattagttggactagcctatcatttatcaagcaatttgttga-aaccctggttgtgtttgatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAGGGCAGGTCCCTAACATAAACGGGAATCCCTTCAACGGAGGACTACCCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatccagataagcaaagcaacctgttgagaaagccttctctgtttaatgcagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
gtttaat putative branch site (score: 4)
ccttctctgttt CT-rich tract
tgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttagggccattacaaggcaattgaaatcaaagaatccaaatatatttatccagataagcaaagcaacctgttgagaaagccttctctgtttaatgcagCTCTGAATGACGCCCTACGAGAAGAAGTTCAGCGGCTTAAGATAGCGGCAGGCCAAGTTCCAAACATGAACGGAAACTCCTTCAATGGAGGACTCCAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA