Sequence
atgc intronic sequence ATGC exonic sequencegtaattcgctatgcctattgagttctcttcaatactttcttgtttagatttgtcaagaagaggggaatagtttcctaatcaatcactcgactaataatttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g49130.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaattcgctatgcctattgagttctcttcaatactttcttgtttagatttgtcaagaagaggggaatagtttcctaatcaatcactcgactaataatttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
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---------------------------------------------------------gtaagccgcatt-tcttctgatc--ctagttg-ctttcaggcacctgtgttg----cttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaattcgctatgcctattgagttctcttcaatactttcttgtttagatttgtcaagaagaggggaatagtttcctaatcaatcactcgactaataatttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
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-----------------gtgagttttagt-attacgccaatcttttatttattcttgatgagcaa------ttctta---------tggtttggaatctttttatattggg-----ctattggcttatatatccgattctctt-----tccagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATCMapped 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|58667255|gb|CK055941.1|CK055941EST: AAACAGTGTCCGGGCAGGCCTTAAGGACATATGTGTACCATGAAATTCTG ATAGGTTATCTTGAGTACTGTAAGCAGCGTGGATTCACCAGTTGTTATATA
genomic: AAACAGTGTCCGGGCAGGCCTTAAGGACATATGTGTACCATGAAATTCTGgtaattcgct ... ctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
ctctaat putative branch site (score: 3)
ctagttttttttct CT-rich tract
ttttgataatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcgctatgcctattgagttctcttcaatactttcttgtttagatttgtcaagaagaggggaatagtttcctaatcaatcactcgactaataatttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA