Sequence
atgc intronic sequence ATGC exonic sequence...taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgtatatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g02060.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018721_T01 (Zea mays), 3'ss of exon 2
--------taattagcccccaaactttttttgcaaataaattaatcaatcaa-tctcttggttaaattaattaatt--aacatgtgtgtgt-atatataaaaaaaaa-aacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
| || | | | | || || || | ||| || | || | || || | | || | || | || | | | ||||||||||||| | ||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
gtacctactggctactgcacgcatggcatctggaactagctctgaaaattaaacccctcaagctagctagctagctctagaatcatcgagtcacggatgagtgtacgtagcagGAGCTACTACCGCTGCACCAACAGCAAGTGCACGGTGAAGAAGCGCGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAG
upper sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G06870.4 (Glycine max), 3'ss of exon 2
-----taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgtatatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
| || | | | | || || | | | | ||| | || |||||||||| || || ||| | ||||||||||||| ||||||| |||||||| ||||||||||||||| |||| || ||||| ||||| ||||| | | || || || || || || || |||
agaacttatgacttcatacatattattcaaactctcaccattaaattgacttcacaacattgataattaattattctg-atgcaattatgtctttttg----cagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGCTCTTCCGAGGACCCAACGATTGTGATTACTACATATGAAGGGCAA
upper sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
taattagcccccaaactttttttgcaaata--aattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgtatata-taaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
|| ||| ||| | || || | | || | ||| | || || | || | | | || | | ||| | | | | ||||||||||||| ||||||| |||||||| ||||||||||||||| |||| || || || ||||| ||||| | | || || ||||| || || || |||
--tataatgaccacactaatattagaactgttatccaaaccctca-ccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
upper sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgt-atatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
| | | | | | || | |||| |||||| ||||| || ||| | | | | | || | | | | ||||||||||| || ||||| ||||||| ||||||||||||||| | || || || || || || || || || | || ||||| || ||||| || |||
------------gtcgtatataagtcatcagtttctttgatcattctcttagttaa--cggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
upper sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0011g00720.t01 (Vitis vinifera), 3'ss of exon 2
-----taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttgg--ttaaattaattaattaacatgtgtgtgtatatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
|| | ||| | ||| | | ||| | || |||| || ||| | || | | | | | | | || ||||||||| ||| ||||||| |||||||| |||||||||||||| | || || |||||||| || || ||| | |||| ||||| || || || ||||||
gggatctcttgggttggaaaaaaatcttgttagctagttatatagcagataaattggatttgtattgaaaaaagattaattttattcacacattttg-------cagGAGCTATTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAAAGAGTTGAACGCTCCTCGGAGGATCCCAGCATCGTAATCACTACATATGAAGGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttggttaaattaattaattaacatgtgtgtgtatatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
aattaac putative branch site (score: 2)
ttaaattaattaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgtatatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt