Sequence
atgc intronic sequence ATGC exonic sequence...tatgagtttgattacagtttgtacctatgcactatgtctttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTTAACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g37430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G350001_T01 (Zea mays), 3'ss of exon 8
tatgagtttgattacagtttgtacctatgcactatgtctttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaac--ctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTT------AACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC--------------------------------------
| | ||| | ||||| | || | ||||||| ||||||||| |||| |||||||||||||||| |||||| |||||| || || ||| ||||||||| ||||||||||||||||||| |||||||
--------------------------------------------------------------gtatgtaacaaaaacatgtatttgaaaaatatccctgcaggtatcaatgccatgaagtgacgtgatcatattgactgatcctggttcaaaattttcagTAAATCAAGGGAGTGCTACACTATTGCCTATTGAAGGAAACTATTCTCGCGGAAATTTGATGCTTCAGAGAATAAAGACATACATT
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G038667_T03 (Zea mays), 3'ss of exon 4
tatgagtttgattacagtttgtacc-tatgcactatgtctttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTT------AACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC
| | | || | | | | ||| | ||| || || | | | | ||| |||||||| || || || ||| | ||||||| | |||||| ||||||||||||||| || ||||||||||||| |||||| |||||| | || ||| |||| |||| ||||||| |||||||||| |
tcttatttgaagtttaaaatatacagtgtgctacattatttaaaacaacagttgtgacatgagttgtttattacctgatcatatctgtagaaccct-gcagGTATCAATGCCAAGAAGCGACTTGATCATATTGACTGATCCTGGTTCAAAAATTTCAGTAAATCAAGGGACTGCTACACTATTGCCAGTTGAAGGAAACT------
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143688_T01 (Zea mays), 3'ss of exon 2
tatgagtttgattacagtttgtacctatgcactatgtc-------tttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTT------AACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC
|| || || || | |||||| | || || || | | || ||| | ||||||||| | || || ||| | ||||||| | |||||| |||||||||||||| |||||||||||||||| |||||| |||||| || || ||| ||||||||| ||||||||||||||||||| |
------cttatttgaagcttaaaaatatgcagtgtgctactttatttccatcaacaattgtgacgtgagttgtttaacacctgatcatatctgtagaaccct-gcagGTATCAATGCCAAGAAGTGACGTGATCATATTGACTGATCCTGGTTCAAAATTTTCAGTAAATCAAGGGAGTGCTACACTATTGCCTATTGAAGGAAACT------
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G038667_T02 (Zea mays), 3'ss of exon 5
tatgagtttgattacagtttgtacctatgcactatgtctttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTT------AACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC--------------------------------------
|||||||| || || || ||| | ||||||| | |||||| ||||||||||||||| || ||||||||||||| |||||| |||||| | || ||| |||| |||| ||||||| |||||||||| |||||||
---------------------------------------------------------atgagttgtttattacctgatcatatctgtagaaccct-gcaggtatcaatgccaagaagcgacttgatcatattgactgatcctggttcaaaaatttcagTAAATCAAGGGACTGCTACACTATTGCCAGTTGAAGGAAACTATTCTCGAGGAAATTTGATGCTTCAGAGAATAAAGACATACATTMapped 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|29671600|gb|CB667875.1|CB667875EST: AGGTGGGAAGGTCCATGGCTATCCTCAACACTTTCATTGGTTTCATACAG GTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAG
genomic: AGGTGGGAAGGTCCATGGCTATCCTCAACACTTTCATTGGTTTCATACAGgtatgtctcc ... acctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTTAACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC
gtttaat putative branch site (score: 4)
cctttgc putative PPT
tttaatatgtgttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgagtttgattacagtttgtacctatgcactatgtctttcactagcgataatgatgctggttgtttaatatgtgttcttatttatagaacctttgcagGTGTCAATGCCAAGAAGCAACGTGATCATATTGACCGATCCTAATTCAAAGTTAACTCATGGGAGTGCTGTGATATTGCCTATTGAAGGAAATTATTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA