Sequence
atgc intronic sequence ATGC exonic sequence...cctagaaatagattccagtgtgtgtttaatctttttaatttaatgttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g43930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G023291_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------cctagaaatagattccagtgtgtgtt--taatctttttaa--tttaatgttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
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gtgagatccatctcccttgctcattccccagaacatcttatttatatttttttttctagataaatcagctgaatggcacaaagtatcatgtagtagtgaatggtgctgttttatgtaagttttgatgcgaaccttgtcgcatgattccacgtctaataccgtgtgttttgatattt--gcagCCTTCTGCTGCGACTACAGACACGAGCTGTGAGTCTGTGGTCACAAGTGGTCAGCACCACCAACAGCAAAACCCAGCAGCTCCGCGTCCTCAACGGGATG
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 2
cctagaaatagattccagtgtgtgtttaatctttttaattt---aatgttgttcgtattactggt-------tcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGG---CAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
||| | ||| ||| |||| ||| |||| | || || || | | | || || | | | || | ||| ||| |||| |||||| | | || ||||||| ||||||||||||||||||| ||||||||| |||| ||||||||||||| || | || ||| | ||||| |
-----------------gtgagcctttcttctctttattttgtgaatgctttttgtgttttttttaatataataatgattcaaccatgttttggtttgaactttgaacagGCTTCTGCAGGTACTACCACAGACAATAGCTGTGAGTCTGTGGTTATGAGTGGTCAAAACCA---ACAGCAAAACCCAACACCTCAGCATCCCAATAGGGATG
upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
--------cctagaaatagattccagtgtgtgtttaatctttttaatttaatgttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
|| ||| || || ||| | | | || ||| | | ||| | || ||| | ||| | | |||| ||| | | ||| | ||| || || |||||||| ||||| ||||||||||| | || ||||| ||||| ||||||||||||||| || | || ||| |||||||| |
tttcaccttctttaaaccagcattaggaagt-tttgctatccattgttcaat--taatagtacttatg-ttcttat---aaatctcatttgctg-gattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATGMapped 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|58665470|gb|CK054156.1|CK054156EST: TGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAAT CCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGT
genomic: TGTCCCGCCTCGTTTACGAGAACGGGTACATGCGGCAGCAGCTCCATAATgtgagattca ... gtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
ctctaat putative branch site (score: 3)
tgttttt putative PPT
atgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctagaaatagattccagtgtgtgtttaatctttttaatttaatgttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- -agaaatag
- - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatg