Sequence
atgc intronic sequence ATGC exonic sequencegtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagtaatttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62810.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 3
gtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagtaatttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG
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gtatttagcaatccaagtccctactccctagtttcgatc--taaacaatcataattatggtattgtt------cttataattgttttgctggaacagATGAATATGATGTTTATACATGGGGTTGGAAAGAATGTGTTCCAACTGGAAGGGTTATTGGAGACCAGTCTTCAGTTGGAACCATGGAAAAGGATGAAAG
upper sequence: LOC_Os01g62810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 1
gtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagtaatttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG
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--------gtatttagcgatccaagttcctagtttcgatcatatacaatcatatttgtggtattgtt------cttataatttttttgctggaacagATGAAGGTGATGTTTATACATGGGGTTGGAAAGAGTGTGTTCCAACTGGAAGGGTTATTGGAGACCAATCTTCAGTTGGAACCAAGGAGAAGGATGAAAG
upper sequence: LOC_Os01g62810.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------------gtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagta-atttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG---
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gtaccttccctttctcagagcatttctttcttatttatctattgagtactatgtgcaaaaaagggggaaaaatggctagaagcttcttgcttgcccatcaaagcttatggagcctttttaagttttttgatggctatttataaaaaatttatcagtatgtcatattcatttctcaatttgc-agACAAAGGTGAAGCATACACATGGGGTTGGAAAGAATGTGTTCCCTCTGGGAAAGTCCTCCTTGAT---TCTACTGGGGTACGCTTTGAAAAGGATTCATTTGGMapped 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|29664300|gb|CB660575.1|CB660575EST: GGCAATAGTGAGAGCTGATGCTGGATGGGCTCATTGTGTTGCAATAACTG ATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAA
genomic: GGCAATAGTGAGAGCTGATGCTGGATGGGCTCATTGTGTTGCAATAACTGgtatactact ... actggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagctcataatttttgtgttactagtaatttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG
ataatttttgtgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactactagttgaacacacatagcgtactttaggacagcaagagctcataatttttgtgttactagtaatttcgtaaatgtcatactggaccagATGAAGGGGATGTCTATACATGGGGTTGGAAAGAATGTGTTCCAACAGGAAGGGTCATTTCTGACCAATCTTCTGGTGGAACTTTGGAAAAAGATGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG