Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaattaccagagaagctgctttttttattattaccatgtaacgctaccaattcttttggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 11
gtaaaaattaccagagaagctgctttttttattattaccatgtaacgctaccaattcttttggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG----
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--atgtactaatatttta-ttgcatcttctctgagaactgagtcctg--accacctcac--------agtttttgaccaagtaaaatttttgcaataacatg---tctatgtgcagGGGAAATTATCTTCCTGCTGACCAGTACTTGAATCA----GAGAAGTCAGACATGACTATTGTGGAAGCTTTCAAAAGGATGCAGGTTGTTCAGCATGAGGAAC
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 7
gtaaaaattaccagagaagctgctttttttattattaccatgtaacgctaccaattcttttggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
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-----atgtacta-atattttattgcatctgctctgagaactgagtcctgaccacctcac-------agtttttgaccaagtattttttttgcaaaaacatg---tctatgtgcagGGGCAATTATCTTCCTGCTGACCAGTACTTGAATCATGCTGAGAAGTCAGACATGACTATTGTGGAAGCTTTCAAAAGGATGCAGGTTGTTCAGCATGAG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 22
----------------------------------------------------------------gtaaaaattaccagagaagctgctttttttat-----------tattaccatgtaacgctaccaattcttttggaagaaactattgtataa---acaaacctggtacaatgataaggtctc--tttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
|| | | | |||| || ||| || || | | || | | | | || | ||| | | || | ||| | | ||| | || | | | | | ||||| | |||||| ||||||||| |||||||||| |||||||| ||||||||||||||| |||||||||||||||||||||||||||| || | |||||
gtacacagtatcacacaaactactacattttgttctagaatattgcttaccagaagttaaaaaaatacattgaatctcagaaacttcttattaaatccaaggagtaatgtactaatattttattgcatctgctctgagaactgagtcctgaccacctcacagtttttgaccaagtaaaatttttgcatatgtgcagGGGCAATTATCTTCCTGCTGACCAGTACTTGAATCATGCTGAGAAGTCAGACATGACTATTGTGGAAGCTTTCAAAAGGATGCAGGTTGTTCAGCATGAG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 21
gtaaaaattaccagagaagctgctttttttattattaccatgtaacgctaccaattcttttggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
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------gtcacca-atattctattgcatctgctctgaatcctaagtcctgaccacctcac-------agtttttgattaattaaaattt-tgcaataacatg-tgtctatgtgcagGGATCATTATCCTCCTGCTGACCAATACTTGAATCATGCTGAGAAGTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
tctctttcttc CT-rich tract
aaactattgtataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaattaccagagaagctgctttttttattattaccatgtaacgctaccaattcttttggaagaaactattgtataaacaaacctggtacaatgataaggtctctttcttcagGGTCCATTATCCTCCTGCTGATGAGTACTTGAACCATGCTGAAAAGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG