Sequence
atgc intronic sequence ATGC exonic sequence...gatgctaattttagttgaaattgcaataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G094039_T03 (Zea mays), 3'ss of exon 2
gatgctaattttagttgaaattg----caataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG
|||| | | ||| | || | || || || | || ||| | || || | | | || |||| |||| | | || || | ||| | |||| |||||||||||||||||||||||||
-atgcagtatgtggttcacatagttcccagtatccttttggacttagatttagtttgata-tatggttatgtttattgacagaatgctttt--tagctttacagATAAAATCTTGAGCAAAATGGGAGAAG
upper sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G366935_T01 (Zea mays), 3'ss of exon 2
--gatgc---taattttagttgaaattgcaataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG-------------------------------------------------------------------------
|||| | | |||| | || || || | || ||| | | || | | | || |||| |||| | || || || ||| | |||||| |||||||||||||||||||||||||
tgaatgcatgtggctcacgttg--ttcccagtatccttttggacttagattgagtttgata-tatggttatgtttattgacacactgctttt--tggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGGTGGGTATCCTCGTTATTATTCTAATGAAGAGGGCTA
upper sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 2
--gatgc---taattttagttgaaattgcaataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG
|||| | | |||| | || || || | || ||| | | || | | | || |||| |||| | || || || ||| | |||||| |||||||||||||||||||||||||
tgaatgcatgtggctcacgttg--ttcccagtatccttttggacttagattgagtttgata-tatggttatgtttattgacacactgctttt--tggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAG
upper sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 2
gatgctaattttagttgaaattg----caataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG-------------------------------------------------------------------------
|||| | | ||| | || | || || || | || ||| | || || | | | || |||| |||| | | || || | ||| | |||| |||||||||||||||||||||||||
-atgcagtatgtggttcacatagttcccagtatccttttggacttagatttagtttgata-tatggttatgtttattgacagaatgctttt--tagctttacagATAAAATCTTGAGCAAAATGGGAGAAGGTTTGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGCTGGGTATCTCCGTTATTATTCTAATGAAGAGGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG
cgttgat putative branch site (score: 5)
ttcttctcttcttggc CT-rich tract
ttgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgctaattttagttgaaattgcaataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA