Sequence
atgc intronic sequence ATGC exonic sequenceCTCAAGATGCGTTGCAGTTCTTGATCAGTTGGATGTCCCGCTTCCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaatgtgtaaactggcgatgtttgcatcaccatctctgaaactattatctctgcatcatctgactactgtccatcaacaaaatttgcacaaattctag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55130.4 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55130.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G879749_T02 (Zea mays), 5'ss of exon 4
CTCAAGATGCGTTGCAGTTCTTGATCAGTTGGATGTCCCGCTTCCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaa--tgtgtaaactggcgatgtt--tgcatcaccatctctgaaacta-ttatctctgcatcatctgactactgtccatcaacaaaatttgcacaaatt-ctag---------
||||||| ||| |||||||| || |||| |||||||| || ||||| ||||| |||||||| ||||||||||| || ||||||||||| || ||| | ||| | | | || || ||| | | || | || || | || | | || | | ||| || || || || |
CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacag
upper sequence: LOC_Os02g55130.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv11s0037g00320.t01 (Vitis vinifera), 5'ss of exon 4
CTCAAGATGCGTTGCAGTTCTTGATCAGTTGGATGTCCCGCTTCCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaatgt------gtaaactggcgatgtttgcatcaccatctctgaaactattatc-tctgcatcatctgactactgtccatcaacaaaatttgcacaaattctag
|||| ||||| || || ||| | || |||||||| | |||||| | || ||| | || ||||||||||||||||| |||||||||||||| | | || || | | || | |||| ||| | || | | | | || | | | | ||||||||| | | |||
CTCAGGATGCTTTAATTTTTTTGGTGAGATGGATGTCAAGATTCCCAAAATACAAACACAGAGAATTCTACATTGCTGGAGAGAGCTATGCTGgtaaccaaaactagaacacatgcagttaattaattaatcactctctaaccctaattgtttacttaatgatcacaagtttaacccacaaaattttattgcaatttagMapped 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|58655220|gb|CK043900.1|CK043900EST: CCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTG GACATTACGTTCCCCAGTTGGCA
genomic: CCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaatgtgta ... caaattctagGACATTACGTTCCCCAGTTGGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCAAGATGCGTTGCAGTTCTTGATCAGTTGGATGTCCCGCTTCCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaatgtgtaaactggcgatgtttgcatcaccatctctgaaactattatctctgcatcatctgactactgtccatcaacaaaatttgcacaaattctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG