Sequence
atgc intronic sequence ATGC exonic sequence...tatttgcatcattattttcaacttttccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCCTTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07340.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G168629_T03 (Zea mays), 3'ss of exon 11
---------------------------------------tatttgcatcat--tattttcaacttttccaagttatagcatct---tatgcagtttattggtgaaa-tacttttacatgcttgaagttgattctac----catgtttagAGCACTGAGCCTATGTTGGCAATCC-TTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC-----------------------
| || | | | || | | || | | | | || | | || | || || || || |||| | | || | || || ||| | ||| || ||| || || ||||||||| ||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |
gtgaggttcatcgaactgcagttagaaaaactggtgccattattataacgtggtaatctggtctcatactgggcactagatatgaatgtgtatcttgtttttgctgctatgtttagcagaaaatatctgcatttagattgcacgttctgtttcctgtccccatgc-atcattctgttttgctttgcagCCCTCGCTGGTTGCTGAAGCAAGAGGTCCCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G053644_T02 (Zea mays), 3'ss of exon 9
------------------------------------------------------tatttgcatcattattttcaactt--ttccaagttatagcat-cttatgcagttta--ttggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCC-TTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC-----------------------
|| || || | ||| | || |||| | | || || | | || | || | || | ||| | |||| | | | ||| || ||| || || ||||||||||||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |
gtgaggttcatcgaactgcagttagaaaaactggtgccattattataacgtggtaatctggtctcatactgggcactagatatgaatgtatatcttgtttttgttgctatgcttagcagaaaaattctgcatttagattgcatgttctgtctcagt--gtctcctgtccccatgc-atcattctgttttgcttttcagCCCTCGCTGGTTGCTGAAGCAAGAGGT-CCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 7
tatttgcatcattattttcaacttttccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCC-TTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC-----------------------
| | | ||| | || | || | || | ||| | |||| | | | ||| || ||| || || ||||||||||||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |
-----------------------------------tgtttttgttgctatgc-ttagcagaaaaattctgcatttagattgcatgttctgtctcagt--gtctcctgtccccatgc-atcattctgttttgcttttcagCCCTCGCTGGTTGCTGAAGCAAGAGGT-CCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 11
tatttgcatcattattttcaacttttccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCCTTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC-----------------------
|| || | ||| || | | || | | || | | | || | ||| | | ||| || | || ||| | | || | ||| ||| |||||||| |||| |||||||| | ||| |||||||||| || |||||||||||||
--------------------------------aatggctatcacttcagcttttcctatagttaagccgaggt--tttacaataactcaaa-atgcagcaattattga--ctgtcttagcactgacat-gcaatgcagTCCTCGATGGTTGTTGAAGCAAGAAGTGTCAAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATTAAGACAAAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 12
tatttgcatcattattttcaacttttccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCCTTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC-----------------------
| || | ||| || | | || | | || | | || ||| | | ||| || || ||| | | || | ||| ||| |||||||| |||| |||||||| | ||| |||||||||| || |||||||||||||
----------------------------------tggctatcacttcagcttttcctatagttaagcccaggt-tttacaataacacataaaatgcagcaattattga--ctgccttagcactgacat-gcaatgcagTCCTCGATGGTTGTTGAAGCAAGAAGTGTCGAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATCAAGACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCCTTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC
agttgat putative branch site (score: 5)
ttctacc CT-rich tract
aaatacttttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttgcatcattattttcaacttttccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgattctaccatgtttagAGCACTGAGCCTATGTTGGCAATCCTTTTGCTTTTCAGCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - tgcatca
- - - - - - - - - - - - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattct