Sequence
atgc intronic sequence ATGC exonic sequencegtgaggttgcttttagtggagcattatcaaatttaaaatactgaatatttgatggaacaggtcatgtaagtgtgtaatgttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g73450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 2
gtgaggttgcttttagtggagcattatcaaatttaaaatactgaatatttgatggaacaggtcatgtaagt--gtgtaa---tgt----tgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
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gttaatcttcttttggtggagcatctttaaacactgacagcagacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG
upper sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 2
gtgaggttgcttttagtggagcattatcaaatttaaaatactg-aatatttgatg----------gaacaggtcatg----------taagtgtgtaatgttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
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gttaaccttcttttggtggagcatgagcatctttaaa-tactgtgatagcagacgagattcatgtgagtgggtcatggaatttaatgtaaatgtgtggt-ctattgcagATTACAATGGCTATTGCAAGAGAGGTTGCTTCTGTCACCAAGCTAGGTGTAGAG
upper sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 2
gtgaggttgcttttagtggagcattatcaaatttaaaatactgaatatttgatggaacaggtcatgtaagt--gtgtaa---tgt----tgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG----------------------------------------------
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gttaatcttcttttggtggagcatctttaaacactgacagcagacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGGTGCCCTCCTGTCTTTTATTTCATTATTGATTACATCTTGTATTACMapped 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|29686224|gb|CB682499.1|CB682499EST: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAG ATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
genomic: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
EST:
gi|88417031|gb|CI573746.1|CI573746EST: TAAGTGGGGAGGGTCTTGGTGGAGATCACACAGAAAATATTGATCCAAAG ATCACGATGGCAATTG
genomic: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTG
EST:
gi|58585704|gb|CF984012.1|CF984012EST: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAG ATCACGATGGCAATTGCAAGAGAGGTTGCTTCTG
genomic: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTG
EST:
gi|29641572|gb|CB646579.1|CB646579EST: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAG ATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
genomic: TAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
EST:
gi|218484425|gb|FG955570.1|FG955570EST: ATCACACAGAAAATATTGATCCAAAG ATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
genomic: ATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
71 (upstream exon),
54 (downstream exon)
Score:
67AGGCTCTAGATCTAAAAAGCCATATAGATGGCAAAGGGTGTTGCTTAAAGTAAGTGGGGAGGCTCTTGCTGGAGATCACACAGAAAATATTGATCCAAAGgtgaggttgc ... gttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaatactgaatatttgatggaacaggtcatgtaagtgtgtaatgttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
atttgat putative branch site (score: 67)
aatatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggttgcttttagtggagcattatcaaatttaaaatactgaatatttgatggaacaggtcatgtaagtgtgtaatgttgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG