Sequence
atgc intronic sequence ATGC exonic sequencegtaacttattatctttgttctttatcaggttatccttagatgcaccattcttaatttatgtttgtagGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 7
gtaacttattatctttgttctttatcaggttatccttagatgcacc----attcttaattta-------------tgtttg-tagGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| | | || | || ||| | |||||||||| | | | || ||||| |||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||
gtcagccaaaattagctatgttcatctgagcgtccttagatgtatgtatgactgttgatttaccctaaggtcctctgtttggcagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 1
gtaacttattatctttgttctttatcaggttatccttagatgcac----cattcttaattta-------------tgtttgt-agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| | || || |||| | | | |||||||| | | | || ||||| |||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||||||||| |||| |||||||||||||
gtgagctaaaattagctatcttgaacctaacgttcttagatgtatgtattactattgatttacactatgatcatctgtttgccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 7
gtaacttattatctttgttctttatcaggttatccttagatgcac----cattcttaattta-------------tgtttgt-agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| | || || |||| | | | |||||||| | | | || ||||| |||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||
gtgagctaaaattagctatcttgaacctaacgttcttagatgtatgtattactgttgatttacactaagatcatctgtttgccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 5
gtaacttattatctttgttctttatcaggttatccttagatgcac----cattcttaattta-------------tgtttgt-agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| | || || |||| | | | |||||||| | | | || ||||| |||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| | ||||||||||| |||| |||||||||||||
gtgagctaaaattagctatcttgaacctaacgttcttagatgtatgtattactattgatttacactatgatcatctgtttgccagGTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAATATAAGAAGCTTTACCTTACAGATCTTGGTTTAG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
------------------------------gtaacttattatctttgttctttatcaggttatcctta-gatgcaccattcttaatttatg---tttgta-----------gGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| | ||| | || ||||| | || || || || | | || ||| ||| | ||| ||||||||||||| ||||||||||| || |||||| ||||||| || ||||||||| |||| || |||||| | |||||||||||||||||| | |
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------gtaacttattatctttgttctttatcaggttatccttagatgcaccattcttaatttatgtttgt--agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
| | | || | || | | | | ||||| ||| | || | |||||||||||||| |||||||||||||| |||||| ||||||| ||||||||| || | ||||||||||| || || ||||| ||||||||| |||
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgtc-atgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------gtaacttattatctttgttctttatcaggtta--tccttagatgcaccattcttaatttatgtttgt--------agGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
|| || | | | | | || | || | || || | | ||| | | || | | | |||||||||||||| |||||||| |||||||||||| | ||||| || |||||| | |||| ||||||||||| | |||||||||||||||||| |
gtgagtactattaataattccatgtttcactttctcagaatcatcctgtctctcttgagcactttcctcaaagtggcttcttcattctgttaattattgtcatcttttttcttcctcaaccaagGTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttctttatcaggttatccttagatgcaccattcttaatttatgtttgtagGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
tcttaat putative branch site (score: 3)
attcttaatttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttattatctttgttctttatcaggttatccttagatgcaccattcttaatttatgtttgtagGTTTGTGCATGGTGATGTGAAACCAGAGAACTTTCTGCTTGGCCAGCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC