Sequence
atgc intronic sequence ATGC exonic sequence...aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcacttgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40090.4 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------aacagaaattttgtccctcgctgctgtttt-cacttttaatggtgaggttttggataat--tagcact-tgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
| | | | || | | | | ||| ||| | | | | ||| | || || |||| ||||||||| | || | |||||| || ||||| ||||| || |||||| |||||||||||||||||||||||| || || || |||||||||||||| ||||||||||| |||||||| |||||||||
gtaagcaaaagaatccagcactctgttgctgctttgatcaccgcagttcaaagccttctggatcttgttaatctttatttaactagtgttgtccatgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttctttt---ctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
aacagaaattttgtccctcgctgctgtttt-cacttttaatggtgaggttttggataat--tagcact-tgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
| | | | || | | | | ||| ||| | | | | ||| | || || |||| ||||||||| | || | |||||| || ||||| ||||| || |||||| |||||||||||||||||||||||| || || || |||||||||||||| ||||||||||| |||||||| |||||||||
-atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgatttcctcttctttt---ctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
-aacagaaattttgtccctcgctgctgttttcactttta--atggtgaggttttggataattagcact-tgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
| ||| || ||| | | || | || || || |||| |||| |||| |||| ||| | ||||| ||||||||| ||||| ||||||||| ||||||||||||||||||||||||||| || || |||||||||||||| ||||||||||| ||||| || |||| ||||
tagtgttgggcctgttggccg-tgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctcttt---gctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcacttgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
| || ||| | || | | || | | | |||| |||||| ||| | || | ||| || |||| ||||||| || ||| ||||||| |||||||||||| |||||||||||||||||| ||||| |||||||| || || ||| | | | || | || || |
-gtaagtgttctgtgct---cttacggagtaacatatcgtttctttgtttaagataat----actaatattggtgtggtt------tttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcactt-gttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
|| |||| | | | | |||| | | | |||| | | ||| ||| | || ||||||| || ||| | || || |||||||||||| |||||||||||||| ||||||||||||||||||||||||| ||| | | || ||| | || || |
-------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaa--gtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 3'ss of exon 4
aacagaaattttgtccctcgctgctgttttcacttttaat--ggtgaggttttggataattagcacttgttttattccagttatttttctttcatg-ctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
| | |||| || | | ||| | || || | | | | | || | ||| ||| | | || | | || | ||| |||||||| || ||| |||||| |||||| || | |||||||||||||||||||| ||||||||||||| ||||| ||||| ||| | || | || || |
--ccatacccctgtcactagtttaagttatagattactatctgattaacatgtaaatgactagt-tttgactgactcaattctgttactgattatgtctgcagTATGTGCATTTTCTTCAACGGAAGTATTCCTTAGGCTCATTCAACCTATTGGGGCATACTGCTCCAGTGCAGGCTGCATCTCTGCTGTTATTAGGACCCTMapped 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|29639689|gb|CB644698.1|CB644698EST: GGCTGCTAGCAGCTGTAATTGCAGTTTGGAGCACAGCACTACAGCAGCAT TACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTG
genomic: GGCTGCTAGCAGCTGTAATTGCAGTTTGGAGCACAGCACTACAGCAGCATgtgagtattt ... catgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTG
EST:
gi|29639690|gb|CB644699.1|CB644699EST: GGCTGCTAGCAGCTGTAATTGCAGTTTGGAGCACAGCACTACAGCAGCAT TACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTG
genomic: GGCTGCTAGCAGCTGTAATTGCAGTTTGGAGCACAGCACTACAGCAGCATgtgagtattt ... catgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttggataattagcacttgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
ttatttttctttcat CT-rich tract
ttatttttctttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcacttgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
-acagaaa
- - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacttg