Sequence
atgc intronic sequence ATGC exonic sequencegtaatttccaccagtcaaatcggatcaacatcaaattccatgcagattgggtaattttacaatctgttcgatccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57320.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G102349_T02 (Zea mays), 3'ss of exon 2
--------------------------------------gtaatttccaccagtcaaatcggatcaacatc----aaattccatg--cagat---tgggtaattttacaatctgttcgat-ccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG
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gtgattcagcaacgcacaattcaccccgatcccatcccccaccccccacccacccacccacgcacacaactgcaaaatcctgtagccaaacatctcgatgttctcacgtgctattcctttccacagGAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG
upper sequence: LOC_Os04g57320.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G102349_T03 (Zea mays), 3'ss of exon 2
--------------------------------------gtaatttccaccagtcaaatcggatcaacatc----aaattccatg--cagat---tgggtaattttacaatctgttcgat-ccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG------
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gtgattcagcaacgcacaattcaccccgatcccatcccccaccccccacccacccacccacgcacacaactgcaaaatcctgtagccaaacatctcgatgttctcacgtgctattcctttccacagGAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGGTGAGGMapped 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|29661402|gb|CB657677.1|CB657677EST: AGGAGAGCTGGGTGGTTAAGCTCGAGCAGTCCGTGAACATTTTCCTCACG GAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCT
genomic: AGGAGAGCTGGGTGGTTAAGCTCGAGCAGTCCGTGAACATTTTCCTCACGgtaatttcca ... cgatccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaacatcaaattccatgcagattgggtaattttacaatctgttcgatccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG
tctgttc CT-rich tract
taattttacaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttccaccagtcaaatcggatcaacatcaaattccatgcagattgggtaattttacaatctgttcgatccgcagGAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA