Sequence
atgc intronic sequence ATGC exonic sequence...cattattcgtatagtgtactacgtatagtatgttgtgtgatgtacacgttttaatctacagaattgtgacattgtgggtgtacgtacatgtgttggatagGTTTCACGTGCTCACGGAGTTTGATGAGGCCAAGAGGAGCTGCCGGAAGCGGCTGGCGGAGCACAACCGTCGCCGGCGGAAGCCGGCGGCGGCGGCGACG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g44860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g44860.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G101499_T01 (Zea mays), 3'ss of exon 1
----cattattcgtatagtgtactacgtatagtatgttgtg--tgatgtacacgttttaatctacagaattgtgacattgtgggtgtacgtacatgtgttggatagGTTTCACGTGCTCACGGAGTTTGATGAGGCCAAGAGGAGCTGCCGGAAGCGGCTGGCGGAGCACAACCGTCGCCGGCGGAAGCCGGCGGCGGCGGCGACG
| ||||| || | | || || ||| | || | | ||||| | || || | |||| | | | ||| ||||||||||||||| ||||||| || |||| |||||||||||||||||| |||||||| ||||||||||| ||||| ||||||||| | | | || |
ccagtgtgattcg-atcatacgcgcgttacgctacgttacggctgcagcaagtgtttttgttcacccgcccgtctctttgttgaaattgtcgcg-----tggctagGTTTCACGTGCTGTCGGAGTTCGACGAGGTCAAGAGGAGCTGCCGGAAACGGCTGGCCGAGCACAACCGCCGCCGCCGGAAGCCGCCCACCACCGCCTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgttttaatctacagaattgtgacattgtgggtgtacgtacatgtgttggatagGTTTCACGTGCTCACGGAGTTTGATGAGGCCAAGAGGAGCTGCCGGAAGCGGCTGGCGGAGCACAACCGTCGCCGGCGGAAGCCGGCGGCGGCGGCGACG
ttttaat putative branch site (score: 3)
ttaatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattattcgtatagtgtactacgtatagtatgttgtgtgatgtacacgttttaatctacagaattgtgacattgtgggtgtacgtacatgtgttggatagGTTTCACGTGCTCACGGAGTTTGATGAGGCCAAGAGGAGCTGCCGGAAGCGGCTGGCGGAGCACAACCGTCGCCGGCGGAAGCCGGCGGCGGCGGCGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - -atgttgt
- - - - - - - - - - - - - - - - - - - - tgtacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg