Sequence
atgc intronic sequence ATGC exonic sequencegtaaagactcctgattccaacaggtttacatacatatgattgtaggaattcctttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g39570.6 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 4
--------------gtaa--agactcctgattccaacaggtttacatacatatgattgtaggaattcctttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
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gtaaaattcaatctttaactagtgtacagattttgaatggtatcccttttcatg--tactgaactgtgtttaatgggcatttgaccaa-tgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAATTTGGAATCAAAGAAATTTGCAGGACAGGAAAA
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 4
gtaaagactcctgattccaacaggtttacatacatatgattgtag----------------gaattcc---tttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
||||| |||| || ||| || |||||| | |||||| ||| | ||| ||| |||||| ||| | |||||| ||||||||||||||||||||| ||| ||||| ||||| || || ||||| || || ||||||||||| || || ||||||
gtaaaaactca-atctctaactagtgtacata-gtttgattgctattcctttttctgtactgaactgtgtgtttaatggacatttgaccaatgt-tagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTAAGGAAATTCGGCATCAAAGAAATTTGCAGGACAGGAAAA
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtaaagactcctgattccaacaggtttacatacatatgatt-gtaggaattcctttgat---gtgtatttg-atcaagttg---tagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
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tccctttaaatctactaagatttgaatttttagactactactatttttttggtcagttcatgctcttataggtcagtgtatttccatgtggatgactcagGTTACTGGAGATCCTGGAAAAATGGTTGCTGTGCAGAGAAATTTAAGCAAGTTTGGAATTAAAGAACTTGCCAGAACTGGAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58601913|gb|CK012441.1|CK012441EST: TTTTCCGAGCGAAAGTTGTTGATATTTCGGAGAACACCCTTACCATCGAG GTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAA
genomic: TTTTCCGAGCGAAAGTTGTTGATATTTCGGAGAACACCCTTACCATCGAGgtaaagactc ... caagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAA
EST:
gi|700146|gb|D46437.1|D46437EST: TTTTCCGAGCGAAAGTTGTTGATATTTCGGAGAACACCCTTACCATCGAG GTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAA
genomic: TTTTCCGAGCGAAAGTTGTTGATATTTCGGAGAACACCCTTACCATCGAGgtaaagactc ... caagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacatacatatgattgtaggaattcctttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
atttgat putative branch site (score: 5)
atacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagactcctgattccaacaggtttacatacatatgattgtaggaattcctttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA