Sequence
atgc intronic sequence ATGC exonic sequence...atattttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42370.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------atat-tttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
| |||| |||| ||||||||||||||| || || || ||||||||||||||||||||||| | ||||||||||||||||||||| | ||||||||||| | |||||| ||||
tttgtgcaaacaagtatttcatatttactgcgttttcttgcaagtatgttttttgggcttcgttgatggcttttcacatttgcgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGTTCCTCATCATCGCACCAGTGGTTGTCTTCTGTGTGT----------------------------------------------------------------------------------
upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------atat-tttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
| | |||| |||| ||||||||||||||| || || || ||||||||||||||||||||||| | |||||||||||| |||||||| | ||||||||||| | |||||| |||
tatgtgcaaacacgtatgtcatacttactgtgttttcttgcaagtatgtttttttggcttcattgatggcttttaacatttgtgtctttgccgtttgcagGAATTCTTCTTGCAGGGAAGATTCATATTTGGGCCTGATGTGAGATCTGTGTTTCTCACTATGATCCTCATCATCGCACCAGTGGTTGTCTTCTGTCTGT----------------------------------------------------------------------------------
upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g00800.t01 (Vitis vinifera), 3'ss of exon 1
--atattttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatcc-atatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
|| | | || |||| | || | | || | | | ||| || | | | || ||| | ||| || |||| | | | | | | | || | || ||| || | | | | | | | | | || | ||| ||| || |
ttttagtaaattttactaaggggtgattttggaatggaatatattcttttatttttgtttcagttttctgaatctcttttttggttgttctgttgtgcagATATTTTTTCTTCAAGGGAGGTTTATATTTGGACCCGATGTGAGATCTCTTGCACTAACCATATT--CCTTATTGTAGCCCCTGTTGCTGTGTTCTGTGTAT-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|29656638|gb|CB652913.1|CB652913EST: GCCACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAAC TGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCG
genomic: GCGACGCCGGCGACCAGCCTAGGGTTTACCAGGTTTGGCGGGGAAGCAACgtaagcactc ... gttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
ttctcac putative branch site (score: 2)
atatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattttgtattttgaaggaattcttcttgcgagggaggtttatatttgggcctgatgtgagatccatatttctcactatgttcctcatcgttgcaccagTGGTGGCCTTCTGCGTGTTTGTCGCCAGACACCTCATTGATGACTTTCCCGGTGATTGGGGTATCTCGGTGATGGTTGTGGTGGTTGTCTTCACCGTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - -cctgatg