Sequence
atgc intronic sequence ATGC exonic sequence...aagacacaccaccatccataattgccatcattattaaacatggatttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g55080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
aagacacaccaccatccataattgccatcattattaaacatggatttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG------------
|| || | || | || |||||| | | | | | || ||| || ||| | | || || ||||| |||||| ||||||||||||||||||||||| ||||| |||||||||||||||||| |||| ||||||||||| ||||| || |||||||||||||||||||||
--tttgcattacgtacggcaactaatataattatt--atgataactagct---agcacaagtagtca----aaattaaggggctaaatttcttgag-caggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
upper sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143204_T03 (Zea mays), 3'ss of exon 2
----------aagacacaccaccatccataattgccatcattattaaacatggatttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
|| || | || | || |||||| | | | | | || ||| || ||| | | || || ||||| |||||| ||||||||||||||||||||||| ||||| |||||||||||||||||| |||| ||||||||||| ||||| || |||||||||||||||||||||
agtttttttttctttgcattacgtacggcaactaatataattatt--atgataactagct---agcacaagtagtca----aaattaaggggctaaatttcttgag-cagGAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAG
upper sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G06870.4 (Glycine max), 3'ss of exon 2
--aagacacaccaccatccataattgccatcattattaaacatggatttg--ttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgact-cagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
|| | | ||| |||| | || | | | ||| | ||| |||| | | | || || | || | || || | | ||||||||||||| ||||||| |||||||| ||||| ||||||||| | || || || |||||||| ||||| | | ||||| || || || || || ||
agaacttatgacttcatacatattattca--aactctcaccattaaattgacttcacaac---attgataattaattattctgatgcaattatgtctttttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGCTCTTCCGAGGACCCAACGATTGTGATTACTACATATGAAGGGCAA
upper sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
aagacacaccaccatccataattgccatcattattaaacatggatttgttcaa--ggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
| | ||||| | | ||| | |||| || | || | || || | || |||| || || | | | | ||||||||||||| ||||||| |||||||| ||||| ||||||||| | || || ||||||||||| ||||| | | ||||| ||||| || || || ||
tataatgaccaca--ctaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
ttttgctt CT-rich tract
acataacaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagacacaccaccatccataattgccatcattattaaacatggatttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG
- - - - - -ccatcca
- - - - - - - - - - - tgccatc
- - - - - - - - - - - - - - - - - - -acatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaaa