Sequence
atgc intronic sequence ATGC exonic sequencegtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g52840.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 4
gtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTG--GCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT------------------------------------
|||| | | ||||||||||| | || | |||| ||| ||| ||| | | | | || | |||| ||| | | |||||| || |||||| | | |||| || ||| ||| |||| | ||||||||||| ||||| ||||| |||||||||||||
gtactgc----cctgctctatcggttgtcattctcgtgattgtttcagtgg-aaacacgcgt---------gcaaattgagtgactg-tctgggtgaataatctgaattggggtttttattctgtgtgttc-ttggtcgcagGTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 4
gtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT
||| ||| | || | | ||| | | | | | || |||| |||| ||| | ||| | ||| || || || | ||| | || | | | | | || |
gta-ggtcgttttttcttcacaagttacgtctaggaacgcttaatgtttgtt-----tgttcgttctagGTTCATTGATATGGCCGAGTCTTTGTGCCAGAAACGAGCA-CTAGAAGCTTTTCGTCT-CAATCCAAACGAATGGGGAG---------------------------------
upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16660 (Selaginella moellendorffii), 3'ss of exon 4
gtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGC-CTGATGGGAGTGAATGATGTGAATTTCTGGTG-GCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT
| ||| | ||| | | || || || | ||||| | | | || | |||| | || | | || | || || | | | | | | | | || ||
-------------------gtaggtcgttttttcttca--caagtgacgtctaggaacgcttaatatttgttcgttctagGTTCATTGATATGGCCGAGTC-TTTGTGCCAGAAACGAGCACTAGAAGCTTTTCGTCTCAATCCAAACGAATGGGGAG-------------------------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|58691682|gb|CK080369.1|CK080369EST: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGA TGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTT
genomic: AACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttga ... gagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT
gtttaat putative branch site (score: 4)
ttaaaaatgtttaatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggttgattgcgttctatcggttgcctttgttcagattatttgggtgttaaaaatgtttaatctgaaagagaaatcagTGCCTGATGGGAGTGAATGATGTGAATTTCTGGTGGCTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT