Sequence
atgc intronic sequence ATGC exonic sequencegtacgcacgcatatatatgcttcccatttgatcaattcaaccacatttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgtatgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g56140.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
gtacgcacgcatatatatg-cttcccatttgatcaattcaaccacatt-----tttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgg-gtgtacatgtgtgtatgag-------cagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
||| | | | ||| | | | |||| || | | | ||| | ||| | | | | ||||| |||| | | | | | | | ||| |||||| |||||||||| |||| || ||||||| |||||||||| ||||||||||| ||||||||||||||||||| |||||||||||||||||||| ||
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
upper sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
------------------------gtacgcacgcatatatatgcttcccatt-tgatcaattcaaccac-atttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgta-tgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
|| ||| | | | | | ||| | || || | | | || | || || | | | | || | | | | | | | ||| || |||||| | ||| || || ||||| | || |||||||||| |||||||||| ||||||||| || |||||| | |||||||||||||| ||| |
gtgagtacctttgtgttctttcttgttggcattc-tgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG
upper sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
------------------------gtacgcacgcatatatatgcttcccatt-tgatcaattcaaccac-atttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgta-tgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
|| ||| | | | | ||| | || || | | | || | || || | | | | ||| | | | | | | | ||| || |||||| | ||| || || ||||| | || || ||||||| |||||||||| ||||||||| || |||||| | |||||||||||||| || |
gtgagtacctttgtgttctttcttgttggcattc-cgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG
upper sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
gtacgcacgcatatatatgcttcccatttgatcaattcaaccacatttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgtatgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
| | | | | || || | | |||| | ||| || || | ||||| |||||| | || || || || || ||||||||||| || | ||||||||| ||||||||||| ||||| || ||||| || |
--------------------------------------------------gtatgttgtgatagttttcattgaat----ttatattcttagttgtttggctg-gttt---cagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgtatgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
ttatgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcacgcatatatatgcttcccatttgatcaattcaaccacatttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgtatgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG