Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttccctctcgccctgcctcgatttctctgaagatttttgctacggttgtcactttgtcaggttgcttctagccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g48160.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G470653_T01 (Zea mays), 3'ss of exon 2
gtgagtttccctctcgccctgcctcgatttctctgaagatttttgctacggttgtcactttgtcaggttgcttctagccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
| ||| | || || || | ||| | | || || | || | || ||| | | ||| | |||||| ||||||||||||||||| |||||||| || || ||||||||||||||||||
----------------------------------------gtgggctctgcttttcttcttcttcatttgt-----gttgtgttgtagcctgcttgacaaag---catggtcttgatgtatcgctcgcagGGCAAGGTGATGAACTGCGGTGGCGGCGGAAGTTGTGGCACTTGCATCGTCGAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G481261_T01 (Zea mays), 3'ss of exon 3
gtgagtttccctctcgccctgcctcgatttctctgaagatttttgctacggttgtcactttgtcaggttgcttctagccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
| |||| || || || | |||| || | ||||| | || | | || | | | | | |||||| ||||||||||||||||| |||||||| || |||||||||||||||||||||
-----------------------------------------------gtgagctctgcttt-tcttcttcatttgtgttgtgctgtagcctgacagacaaagc-gtggtcttgctgtatcgctc--gcagGGTAAGGTGATGAACTGCGGTGGCGGCGGAAGTTGCGGCACTTGCATCGTCGAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtttccctctcgccctgcctcgatttctctgaagatttttgctacggttgtcactttgtcaggttgcttctagccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
|| | | || | | || | || | || || ||| || || | | | | | | ||| ||| ||||||||| ||||||||||||| ||||| || |||||||| |||||||| || |||
----------------------------ttacatatgatatggtggggcagctgggaattgatt--ttttgttgagttgaagtcagtgtacaatacataacttgaaaagatgggattgagctttgaacagGGGAAGTTGATGAACTGCGGGGGCGGTGGAAGCTGCGGAACTTGCATTGTTGAGMapped 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|88485358|gb|CI422629.1|CI422629EST: TCCTCCGGGACGTCATGGTCGAGAACAAGATCGAGCTCTACGCGGCATAT GGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTC
genomic: TCCTCCGGGACGTCATGGTCGAGAACAAGATCGAGCTCTACGCGGCATATgtgagtttcc ... gtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTC
EST:
gi|86528962|gb|CI169168.1|CI169168EST: TCCTCCGGGACGTCATGGTCGAGAACAAGATCGAGCTCTACGCGGCATAT GGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTC
genomic: TCCTCCGGGACGTCATGGTCGAGAACAAGATCGAGCTCTACGCGGCATATgtgagtttcc ... gtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
gtgtaac putative branch site (score: 3)
ttgttttt putative PPT
ttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttccctctcgccctgcctcgatttctctgaagatttttgctacggttgtcactttgtcaggttgcttctagccaagctgcagtgtaacagagagagttgcattgctgttttgttgtttttgcagGGGAAGGTGATGAACTGCGGCGGCGGCGGCAGCTGCGGCACTTGCATCGTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC