Sequence
atgc intronic sequence ATGC exonic sequencegtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 17
gtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcat-tgctaataaacagaatggattctggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
| ||||| | ||| | || |||| || || || | | || | || | | | | | |||| |||| |||||||||| || ||||| || ||||||||||| |||||||||||||||||||| || |||||||||||||||
----------------------tatttgtcgcggtttagttcaaaaatgagctagcgggcgacaaatattcgagaacggatgtagtatattataagacctctcattcctatttactgttcagGCTATCGTCATAGAAGCACAGAGTGAATCTAAATGGAAGCAGTTGGGTGAACTCGCCATGTCCACAGGCAAG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 18
gtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctga---aaggtcttccatgctgtgaagttcattgctaataaacaga------atggattct---ggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
|||| | || |||| | |||| | | | | || || || ||| | || | | | | ||| |||| |||| | ||| ||| | |||| |||| ||||||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||||||
gtactggttatattgtcattaattttcttctaatgctgtgga--ctatattttgagttattgtatactgcattactgaaaaaattactaagtaacatatattatatgacctctcatgactatttactgtacagGCTATCGCCATAGAAGCACAAAGTGAATCTAAATGGAAGCAGTTGGGCGAACTTGCCATGTCCACAGGCAAG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 7
gtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctga---aaggtcttccatgctgtgaagttcattgctaataaacaga------atggattct---ggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
|||| | || |||| | |||| | | | | || || || ||| | || | | | | | |||| |||| | ||| ||| | |||| |||| ||||||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||||||||
gtactggttatattgtcattaattttcttctaataccgtgga--ctatattttgagttattgtatactgcattactggaaaaaatactaagtaacatatattatatgacctctcatgactatttactgtacagGCTATCGCCATAGAAGCACAAAGTGAATCTAAATGGAAGCAGTTGGGCGAACTTGCCATGTCCACAGGCAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|2443004|gb|C74775.1|C74775EST: ATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGATGTTGCAAAG GCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTNGGTGAA
genomic: ATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAATTAGAAGTTGCAAAGgtacagaaca ... ttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
tgctaat putative branch site (score: 2)
cattttct putative PPT
taataaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagaacatgttgtattgtgtttttgttccacattattgaaataatgttctgaaaggtcttccatgctgtgaagttcattgctaataaacagaatggattctggacattttctgtgcagGCTATCGCGATGGAAGCGCAAAGTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG