Sequence
atgc intronic sequence ATGC exonic sequence...agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
----agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
||| | ||| ||| | ||| | || | || | | | || | || || | ||| ||| | ||| || ||||| ||||||||||| ||| |||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||||||||
ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctg--gcagccctggtgttca--ctaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G143804_T01 (Zea mays), 3'ss of exon 3
----agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
|| | ||| || | || | | || | | | | | ||| | || || | ||| ||||||||||| | ||||| ||||| ||||| ||| ||||||||||||| ||||||| || ||||||| |||||| |||||||||| |||||||||||||||||||||||||| |
cctgtatttgtttctattgtctgtggccacgtgtaataagaaaacccttgttg--gcagccctggtgttca--ctaactctcttgtgttattttatgctcaaagGAATGGGTAACCGACAATTCTTTTATCATATCGCCAAGGACCACTTTTGAAGACAGTGTCTGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATGG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 7
agcttagatatatactcctttgctataccttattatcata--tcgtattt----gcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
|| | || | | | | || | | | | | || |||| | | ||||| | | | | | ||| || | ||| |||| |||||||| |||| ||| || || |||||||| || ||||| ||||||||||| || || ||||||||||| ||||||| |||||||| || || |
---ctactcctgccttcttgagtttgaaatttgcggaaaagtttgcagttagaagcaaaattactgaaaaacctctataatg-ttagtgcattt--ttgttttcagGAATGGGTGACAGATAGTCCATTCATAATATCACCTAGAATTACTTTTGAAGTCAGCGTGCGCCTTCTTGGAGGGCTGATGGCCTTGGGATACACAATTG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
-agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
| | ||| | | |||||| | || | ||||| | ||| | ||||| ||||| | ||| || | ||| |||| |||||||| ||||| || ||| ||||||||||||| ||||| ||||| |||||||| || |||||||| || | ||||| |||||||| || ||||
tttgtgttttgcatattatatatatataccaattccccacacttgatttgtggagaatttttacacggtgttaactaattgatgtc-ttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
-agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
|| ||||||| | | | | || || || | | | || ||| | | ||||| ||||| | ||| ||| | ||| |||| |||||||| |||||||| ||| ||||||||||||| ||||| ||||| |||||||| || |||||||| || | ||||| |||||||| || ||||
atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtc-ttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 6
agcttagatatatactcctttgctataccttattatcatatcgtatttgcaa-taattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
|| || | || | | | | | | | | | | || || || || || || || | || ||| |||| |||||||| |||| ||| || || |||||||| || ||||| ||||| ||||| || || ||||||||||| ||||||| |||||||| || || |
-ctataactaccttcttgagtttgaaatttgctgagaagtttgcagttagaagcaaaattactgcaaaaactctatagtgatagtgcattattgttttcagGAATGGGTGACAGATAGTCCATTCATAATATCACCTAGAATTACTTTTGAGGTCAGCGTGCGCCTTCTTGGAGGGCTGATGGCCTTGGGATACACAATTG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttga--agGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
| | ||| | | | || | | || | ||| | | || | || | | | | || | | ||||| ||| | | | | |||| ||||| || |||| ||||||| ||||||| ||||||||||| ||||||||||||||||| || ||||| || | |||||||||||||| || ||||
gtttgttcagagtttattttccatgttctcatcaatatgactattcaata-tctggaaaagctgacaatccctctgattctggtaagatgcttag-tatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataat--tttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
| ||| | | ||| || || || |||||||| | || | ||| ||| | || || | | | | | ||| | | || |||||||||| || ||| ||| ||||| |||||||| || || || |||||||| |||||||||||||||||||| || |||||| |||| ||||| || |
gtttggccaatacctgtccagactagtttttcttctgtaaacaccat-atcatatcaaagctgaacgaatggtttattaatt-tgatgaatgattaccgttctatgtg-ttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 5
--agcttagatatatactcctttgcta-taccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
| ||| | | | || |||| || | || |||| | | | || | | | || || | | ||| | | |||| | ||| ||||| || |||||||| ||| | ||||||||||| || || |||||||||||||| || |||||||| || | ||||| ||||| || || ||||
acaccttgtctttgt-ctggtttgttaacttcctaaggtcatttta-gtccatgagaaatacgcgagacttgcccaatctgatcagttggttctcatttca-gGAATGGGTTACTGATAATCCATTTGTTATATCACCAAGAATAACTTTTGAAGTCAGTGTGCGGCTTCTTGGTGGGCTAATGGCCTTGGGGTACACAATAGMapped 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|218492625|gb|FG962240.1|FG962240EST: CTTATTTGAGAATGAGGAATAGGGAAGGGAAATATAATCTGATGTTTGAG GAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAA
genomic: CTTATTTGAGAATGAGGAATAGGGAAGGGAAATATAATCTGATGTTTGAGgtatgcaatt ... taatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAA
EST:
gi|428928|gb|D25084.1|D25084EST: CTTATTTGAGAATGAGGAATAGGGAAGGGAAATATAATCTGATGTTTGAG GAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAA
genomic: CTTATTTGAGAATGAGGAATAGGGAAGGGAAATATAATCTGATGTTTGAGgtatgcaatt ... taatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
aataattttgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG