Sequence
atgc intronic sequence ATGC exonic sequencegtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAGCTGGACGCCCGCCCTCCCGGCCGCCACGACGCGCGCGACCCGGAGCTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g03770.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g03770.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G452178_T01 (Zea mays), 3'ss of exon 1
gtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccat--ccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAGCTGGACGCCCGCCCTCCCGGCCGCCACGACGCGCGCGACCCGGAGCTCG
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-----tccgcgcgcctgtcgcgtcgcc----tcgctcctcacgaatcacgatcaccctcacatggtggctacg-aaatgac-gcaagcacgcgcgcgctgtgacactgcagGTGGGCGCGCCGCCGGACCTGCTGGAGAGGCTGACGGCCATGGCGGCGAAGCTGGACGCGCGCCCGCCGGGCCGCCACGGGCCGCGCGACCCGGAGCTGG
upper sequence: LOC_Os07g03770.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028041_T01 (Zea mays), 3'ss of exon 1
---gtatatacgctcgattaattctt-ctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAGCTGGACGCCCGCCCTCCCGGCCGCCACGACGCGCGCGACCCGGAGCTCG
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aatctatccacgcctgtcgcgtcctcacgctcaccctcacagtcacaggacagcacggtggctatgaa---atgatgcgcg-cgctgtgtctgtg---------tgattgcagGTGGGCGCGCCGCCGGACGTGCTGGAGAGGCTGACGGCCATGGCGGCAAAGCTGGACGCGCGCCCGCCGGGCCGCCACGAGCCGCGCGACCCGGAGCTGGMapped 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|58591417|gb|CF989725.1|CF989725EST: CTCCGCCCTCCTCGCAG-CTACCTCGACTGCCAGAAA GTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCGACGGCGGCAAAG
genomic: CTCCGCCCTCCTCGCAGCCTACCTCGACTGCCAGAAAgtatatacgc ... atccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattatctatcgatcatatatatcactgcaattttgatccatccatccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAGCTGGACGCCCGCCCTCCCGGCCGCCACGACGCGCGCGACCCGGAGCTCG
ttttgat putative branch site (score: 4)
tccatcc putative PPT
atcatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatacgctcgattaattcttctccgattttgttgaacaaaatactccgtagtaattatctatcgatcatatatatcactgcaattttgatccatccatccatccagGTCGGAGCGCCGCCGGAGGTGCTGGAGAGGCTGACCGCCACGGCGGCAAAGCTGGACGCCCGCCCTCCCGGCCGCCACGACGCGCGCGACCCGGAGCTCG
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