Sequence
atgc intronic sequence ATGC exonic sequence...tttttttttctcctatagttttaatttcctaagctaaggcaaattgctcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03822.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G458888_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------tttttttttct-cctatagttttaatttcctaagctaaggcaaattgctcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
| | |||||| | || |||||| | || | | || | | | | | | | | | ||| || || || || ||| |||| |||||||| ||||| ||| |||||||||| ||||||||||| ||||| |||||| ||||||| ||||||||| |||| ||| |||||||||| | |
gtgaggaaggatttaagttttcccattcgtacagacgagatagtggcgtttacttataaagttgcgtttaaatgaatctccttttctgcttagagttttcggactgtcc-cttttgtagatggtgcatactgtttcggtgtgtgaactataatgaagcggttagttctttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
upper sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 2
tttttttttctcctatagttttaatttcctaagctaaggcaaattgc-tcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
||| ||| | | |||| || | | |||||| || | | | ||| || | ||||| | | | || ||| ||| |||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||| |||| ||| |||||||||| | |
tttcggcttcaagtttcattttg-ttccttttgctaagataatgcgtattgtttcagtgtgagagctgtactgtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTTMapped 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|58596309|gb|CK006837.1|CK006837EST: AAAGCCGAAGCTTCATCGTCTAGGGTGCCTTCTTGCCCAGCCAAG GTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTC
genomic: AAAGCCGAAGCTTCATCGTCTAGGGTGCCTTCTTGCCCAGCCAAGgtgagagggc ... ttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
cactgac putative branch site (score: 2)
tatttcttttc putative PPT
tatttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttttctcctatagttttaatttcctaagctaaggcaaattgctcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
- - - - - - - - - - - - - - - - - - - - - - -gctcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacac