Sequence
atgc intronic sequence ATGC exonic sequencegtgggttccccgctcccgattccctcattttttttcttccattcggtttgctccgcgggtttggtgacgtgtgtgcttgttgttgttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15040.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 2
gtgggttccccgctcccgattccctcattttttttcttccattcggtttgctccgcgggtttggtgacgtgtgtgcttgttgttgttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG
||| |||| | |||| || ||||| | || | |||| | || || ||| ||| |||| || || |||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |
gtgagttctgatttaccgagtcg-tcattcctgttgct------ggttgaagttgttggatt--tgatgtg-gtgccccgcgtg-------tgttgcagCAATTGGATTCAACGTTGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTATGGGATCTTG
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G24765.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgggttccccgctcccgattccctcattttttttcttccattcggtttgctccgcgggtt-tggtgacgtgtgtgcttgttgttgttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG
| | || | ||| || | | | | | | | | || | | | | ||| | | | |||||| ||||| || ||||| ||||| |||||||||||||| |||||||| || ||||||||| | |
-------gtatgtatctaatctctcgattattgtatagattatggatctagtttatgtatcgtgattttacgaattttggttttgatctgatctttgcagCTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAG
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtgggttccccgctcccgattccctcattttttttctt-----ccattcggtttgctccgcgggtttggtgacg-tgtgtgcttgttgttg---------ttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG
| || | | | | || | |||| || || | | |||| | | | ||| | | | ||| | | | | ||| |||||| |||||||| || ||||| || || ||||| |||||||||||||| |||||||||||||| |
gtatgtgtttgcttttgggtttttgtttttgtttttttttttttggtttttgggggttttgagttttgttttatctatgtagtgttgatttccaattgatctcaaattcctattcgttttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAGTCTGGGATCTGG
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP03455 (Chlamydomonas reinhardtii), 3'ss of exon 2
--gtgggttccccgctcccgattccctcattttttttcttccattcggtttgctccgcgggtttggtg-acgtgtgtgcttgttgttgttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG-------------------------------------------
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ccacatcgctggggtgtgtgggacactcgagcggccccaccgatgcatctgactcc-tgcccttggcacgcatgtgcgccgcgcaccaccacgccac-gcag-Mapped 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|88383993|gb|CI631883.1|CI631883EST: ATCGGCTGCAGATGGGGGAGGTCGTCTCCACGATCCCAA CGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAG
genomic: ATCGGCTGCAGATGGGGGAGGTCGTCTCCACGATCCCAAgtgggttccc ... gttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggttccccgctcccgattccctcattttttttcttccattcggtttgctccgcgggtttggtgacgtgtgtgcttgttgttgttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA