Sequence
atgc intronic sequence ATGC exonic sequence...gaagttctactttttgaactacaattttataattggtgattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g07440.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115451_T02 (Zea mays), 3'ss of exon 3
gaagttctactttttgaactacaattttataattggtga--ttgagatccttatca---ttacatga--ctgtttggc-tcaaatg-ttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
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---------acttttgaattacatattgattttaaatgaagtttccttttttattaattctaaatgaagcttcccaccattgcatgatcgtaatttcttcaattttcagGGTATATATGGTTATCCCATTGAGATTCAAGCCCTATTCTATATGGCATTAAGATGTGCTCTCCAAATGCTCAAGCCAGAGGGCGAAGGGAAGGATTTCA
upper sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007277_T01 (Zea mays), 3'ss of exon 3
-----gaagttctactttttgaactacaattttataattggtgattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
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ccctacaagttctcttattgtttgtcctacttttgaattacatattaa----tttcaaatgaagcttcttgtcagtgcatg-attgtaattactgcaattatcagGGTATATATGGTTATCCCATTGAAATCCAAGCCCTATTCTACATGGCTTTAAGATGTGCTCTCCAAATGCTCAAGCCAGAGGGTGAAGGGAAGGATTTCA
upper sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G35890.2 (Glycine max), 3'ss of exon 3
gaagttctacttttt--gaactacaattttataattggt-gattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTG---AAGGGAAGGATTTCA
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---tttcaagctccctggagttaagctttcattcttatttgactgattttgaagaacttgcatattttattaattgtttcgtcctcttccttttttcttgcagGGTATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGGAAGGAAT---
upper sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
gaagttctactttttgaactacaatttt---ataattgg-tgattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTG---AAGGGAAGGATTTCA
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----tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT---
upper sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0072g01040.t01 (Vitis vinifera), 3'ss of exon 3
gaagttctactttttgaactacaattttataattggtgattg-agatccttatcattacatgactgtttggctcaaatgttaaatctactattatttc--cagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
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---gttcattattttcaagagctttgtagttgtcagaaagtacatattaacatgtatgaatcacatgttaacacgtttgatcacatggattttattttgacagGGTATTTATGGTTATCCAATTGAAATTCAAGCACTTTTCTTCATGGCACTGAGATGTGCTTTGGCAATGCTAAAACAAGACTCTGAAGGTAAAGAATGTAMapped 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|29659329|gb|CB655604.1|CB655604EST: TCCCAACTCTGCTCTGCACAGATGGCTGCTCAATGATAGATCGTCGAATG GGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTG
genomic: TCCCAACTCTGCTCTGCACAGATGGCTGCTCAATGATAGATCGTCGAATGgtatgagctt ... ttatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
ttatttcc CT-rich tract
aaatgttaaatctact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagttctactttttgaactacaattttataattggtgattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTGAAGGGAAGGATTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - aactaca
- - - - - - - - - - - - - - - - -tggtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg