Sequence
atgc intronic sequence ATGC exonic sequencegtgagttccttggttaatttggaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G140328_T04 (Zea mays), 3'ss of exon 10
gtgagttccttg-----gttaatttggaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
|| || | || | | ||||||| ||| | |||| ||| || || || || | | | ||||| |||||||| ||||||||||| || || ||||| |||||||| ||||| |||||||| || || |||||||| ||||||
gtaagctactccaatatgctgctttggaagtaacacactttacctgtgaacctaacttggccacatgtgggttatttgaagGTACACAAAGATCAAAAGTCGCCATTTCTAATGTCAGGTTGCAAAGTTGCCGATGGCTATGGCACAATGCTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 10
gtgagttccttggttaa-----tttggaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
|| |||| || ||| |||||| ||| | | | || || || || || | | || |||||||| ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| || ||||||
gtaagttactccattatgcagccttggaagtaacaca---catacatgaacctaacttggccaaatggggactatttgaagGTACACAAAGATCAGAAATCACCATTTCTAATGTCAGGTTGCAAAGTTGCCGATGGATATGGAACAATGCTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 11
------gtgagttccttggtta--atttggaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGA--AATCA-CCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
| | | ||| ||| ||||| ||| |||| | | | || ||| ||| | ||| | | ||||||| ||| | | || || ||||||||||||||||| ||||||||||| || || |||| || ||| ||
gtatactttattctcttccttagcatttgcaacaaataccatctttgcatttcatgtgttctgaaaaagct--gtttctcgcagGTTCAAAAAAACTCTACTAAGCATCCATTCCTAATGTCTGGCTGTAAAGTTGCAGATGGCAATGGGACAATGTTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagttcctt--ggttaa---tttggaactaatatggt----ttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
|||||||| || |||| | || || | |||||| || | | | | | || | |||| ||| |||||||||| ||||| ||||| || || ||||||||||| |||||||| |||||||| || | ||||||
gtgagttcattatggttctgcttgtgcaatttttatggtcatcttccctttctatttgctaacacagacctttg----tttgcagGTTCACAAGGATCAAAAATCCCCTTTTCTAATGTCTGGCTGTAAAGTAGCTGACGGAGTCGGTAACATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
ttaattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttccttggttaatttggaactaatatggtttaggtgttaagctcacactgcaaagttttggttaattgaagGTTCACAAAGATCAGAAATCACCATTCCTAATGTCTGGTTGTAAAGTTGCTGACGGGTATGGCACTATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG