Sequence
atgc intronic sequence ATGC exonic sequence...ccacctccatgctcgcgagctttagtgagcacagtgaattaaagcgaagcgatgtgaaaatataattgtgtacatgtgtgttgatggatgtgtgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72020.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G060723_T01 (Zea mays), 3'ss of exon 1
ccacctccatgctcgc---gagctttagtgagcaca---gtgaattaaagcgaagcgatgtgaaaatataattgtgtacatgtgtgttgatggatgtgtgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
||| || ||| | || | || |||| | || | | | | | | | ||||| | | |||| || | |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||
--acccacagtctcacagtgaaagtgagcgagcttacacatgcgcgcagacttactgttactgatgaagaattgca-atgcttccgttgctgcgcgcttgcagAAGCAGCTGGCCGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTGATGGCGTCGCGGAAGCAGGACCTGCACCAGCTGTGGACCACGT---
upper sequence: LOC_Os01g72020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G039867_T01 (Zea mays), 3'ss of exon 1
--ccac-ctccatgctcgcgagctttagtgagcacagtgaattaaagcgaagcgatgtgaaaatataattgtgtacatgtgtgttgatgg-atgtgtgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
| || || || || || ||||| | | | || ||| || || | | | | || |||| || | ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||
tgctacactgagtgagtcacagtgaaagcgagcaagcttgcacatggagagtgactgttgaagaattcattcattcct-tgggttgttgtcgcgctcgcagAAGCAGCTGGCCGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTGATGGCGTCGCGGAAGCAGGACCTGCACCAGCTGTGGACCACGT---
upper sequence: LOC_Os01g72020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0007g05740.t01 (Vitis vinifera), 3'ss of exon 1
-ccacctccatgctcgcgagctttagtgagcacagtgaattaaagcgaagcgatgtgaaaatataattgtgtacatgtgtgttgatggatgtg---tgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
| ||| ||| | | || | || || | | || | | || | || ||| | ||| | | | |||||||||| ||||| |||||||||||||||| ||||| || || || ||||| || || || || || || ||||| ||| |||||||||| ||||| || |
acaacccacattttttccagtgcaaaaacttccaaaacatcattttggtttga-ataattccattcacgaatatttgtttattgctttttacgggttgcagAAGCAATTGGCAAGCATGGTGGAGAAGGCCTCGATTGAAGATGTAATGAAAGTACTAATAGCTTCAAGAAAGCAAGACATGCACCAGCTTTGGACTACCT---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|7608717|gb|AU090498.1|AU090498EST: TCGCCGCCGCGCGCT-CTTCGGCGTCGAGGAGCTCGCCCTCCTCACCCAGAAG
genomic: TCGCCGCCGCGCGCTCCTTCGGCGTCGAGGAGCTCGCCCTCCTCACCC---AGgtaatcaatc ... tgtgcaga
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagcgatgtgaaaatataattgtgtacatgtgtgttgatggatgtgtgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
tgttgat putative branch site (score: 4)
atgtgaaaatataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccacctccatgctcgcgagctttagtgagcacagtgaattaaagcgaagcgatgtgaaaatataattgtgtacatgtgtgttgatggatgtgtgcagaagCAGCTGGCAGGCATGGTGGAGAAGGCGTCGATCGAGGACGTGATGAAGGTGCTTATGGCGTCGAGGAAGCAGGACCTGCACCAGCTGTGGACAACGTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - - -cgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg