Sequence
atgc intronic sequence ATGC exonic sequence...atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtcttctagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g06560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 4
atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtcttc-tagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT----
| | | | | || || | | | | || |||| | | | | | | | | || | | ||||||||||| || ||| | |||||||||||||| || ||||||||||||||||| || |||||| || |||| |||||||| || || ||||||| |
-----------gtatgggcagcaatcttttccttagtgaaagcattgttcttatcttagctgcttcgacctctaatctcttatcacctactttcattgcagGCTGGTGACTCTACTCCAGAGGAGCTTGCCACCGCTACCCAGGTCCAGGGTGACTA----CATGCCATTTACTCGTGGTGAGAAACGTTCAGTTGAGGTTGTGA
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G145280_T02 (Zea mays), 3'ss of exon 4
atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtcttc-tagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT----
| | || || | | | || || | | | | || |||| | | | | | | | | || | | ||||||||||| || ||| | |||||||||||||| || ||||||||||||||||| || |||||| || |||| |||||||| || || ||||||| |
---gttaaggtatg--ggcagcaatcttttccttagtgaaagcattgttcttatcttagctgcttcgacctctaatctcttatcacctactttcattgcagGCTGGTGACTCTACTCCAGAGGAGCTTGCCACCGCTACCCAGGTCCAGGGTGACTA----CATGCCATTTACTCGTGGTGAGAAACGTTCAGTTGAGGTTGTGA
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G409407_T01 (Zea mays), 3'ss of exon 4
------atggctgcagtttgttg--tccctgactccttgtatatgtttatcgaaggtattgtcttctagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT----
| | | ||| || | ||| ||||| | | | | || | || | | | || || | | || | | ||||| || || || ||| | |||||||||||||| |||||||||||||||||||| || |||||||||| |||| |||||||||||||| || |||| |
gtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggttgttttgacttctaatcccttgtggcctaccttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGTGACTA----CATGCCTATTACTCGTGGTGAGAAGCGCTCAGTCGAGGTTGTGA
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 4
atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtcttcta--gatctggttttgagcttgattgt-gctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT----
| | ||| | | ||||| | || | | | | ||||| ||||||| | | || | | | | || | | || |||| ||||||||||| || ||| ||||||||| ||||||| |||||||| |||||||| || |||||| ||| ||||||||||||||||||| || |||| |
gtatgagtagtcatcttttcctgaacaat--taagtatctcttgaaggcattgtctctggctgctttgatctcaaaatcccttatcacctacttttgttgcagGCTGGTGACTCTACTCTGGAGGAGCTTACCACTGCTACCCAGGTACAGGGTGACTA----CATGCCAATTACTCGCGGTGAGAAGCGCTCTGTAGAGGTTGTGA
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 5
-------atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtctt---ctagatctggttttgagcttgattgtgctagc-tcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT-------
| | | || | | | || || || | | | | | | || || || | | || | || | ||||||||||||| ||| ||||||||||||| | ||| || || |||||||||| || | ||||||||| | ||||||| | ||||| |
gtaattcagatgttccattatctattttgattgtggtaggcattttcatttctgatgaaggttgaaatgaaagatgtttgtgtgtcatgtgacactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACACAAGTCCAGGGTGCTTTCT----TGCCTATTGT---GAGGGAGAAGCCAACTGTTGAACTTGTAAAGG
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G14640.2 (Glycine max), 3'ss of exon 4
---------------------atggctgcagtttgttgtccctgactc--cttgtatatgtttatcgaaggt-attgtcttctagatctggttttgagcttgattgtgctagctcttgtgtc--agGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT-------
|| | | | ||| | | || || || |||| | || ||| | | || || | || | | | || | | || | | ||||||||||||| ||| ||||||||||||| | ||| || || ||||||||| || | ||||||||| | ||||||| | ||||| |
gtaatacagatgttcaattatctgttttgattgtgtgggcattgtcttaattttgatatcatcatttctggtgaaaggtaaaaaggaatgatgtttgtgtgaaatctgactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACGCAAGTCCAGGGTTCTTTCT----TGCCTATTGT---GAGGGAGAAGCCAACTGTTGAACTTGTAAAGG
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G34760.2 (Glycine max), 3'ss of exon 4
atggctgcagttt-gttgtccctgactccttgtatatgtttatcgaaggtattgtcttct------agatctggttttgagcttgattgtgc------tagctcttgtgtc-------agGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT-------
| | | || | ||| || | | | | | || || | | ||| ||| || | | | || | | || ||||| | | || ||| ||||||||||||| ||| ||||||||||||| | ||| || || |||||||||| || | ||||||||| | ||||||| | ||||| |
gttaaggtaattcagatgttcc--attatctattt-tgattgtggtaggcattttcatttctgatgaaggttgaaatgaaagatgtttgtgtgtcatgtgacactgttgttttattgtagGCTGGTGATTCTACTCCCGAGGAGCTTGCAAATGCAACACAAGTCCAGGGTGCTTTCT----TGCCTATTGT---GAGGGAGAAGCCAACTGTTGAACTTGTAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtattgtcttctagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT
gcttgat putative branch site (score: 5)
ctcttgt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggctgcagtttgttgtccctgactccttgtatatgtttatcgaaggtattgtcttctagatctggttttgagcttgattgtgctagctcttgtgtcagGCTGGTGATTCCACTGCCGAGGAGCTTGCCACTGCCACCCAGGTCCAGGGTGATTAATTACATGCCTATTGCTCGCGGTGAGAAGCGCTCGGTTGAGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- -gctgcag
- - - - - - - - gtccctg
- - - - - - - - - - - - ctccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctagc