Sequence
atgc intronic sequence ATGC exonic sequence...tatcaattaaactatgttatgaacaaggacaacggtttggtctttctgctgacgattgattatagtactaaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27350.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G458441_T01 (Zea mays), 3'ss of exon 5
tatcaattaaactatgttatgaacaaggacaacggtttggtctttctgctgacgattgattatagtac-taaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
|| | |||| | || | || || | | | | | | | | || || | || || | | ||||||||||||||||| || ||||||||||||||||| | || || ||||||||| ||||||| |||||||| ||||| |||||||| ||||||||||||
taatatgcaaacca-attttaaattcatgcagtcatcatggcaatgaataaaaatgtcgtattgatatgtatttaattactacctgtttcctttctatcagGTACATCCCATTACTAAAGGAGACATTTATGTTCCCACAAAGCTTGTGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGG---------
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G064212_T02 (Zea mays), 3'ss of exon 5
---tatcaattaaactatgt-tatgaacaaggacaacggtttggtctttctgctgacgattgattatagtactaaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
||| | ||| || || | | | ||| | |||||||||| | | ||| ||| | | ||||| ||||||||||||||||| || ||||||||||||||||| | || || ||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||
tgcagtcatcatggcaatgaataaaaatgtcgtctaataattgatgtttctgctgatgtattgatatgtatttaattactacctgtttc----ctttctatcagGTACATCCCATTACTAAAGGAGACATTTATGTTCCCACAAAGCTTGGGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGAT
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G442425_T01 (Zea mays), 3'ss of exon 4
tatcaattaaactatgttatgaacaaggacaacggtttggtctttctgctgacgattgattatagtac-taaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
|| | |||| | || | || || | | | | | | | | || || | || || | ||||||||||||||||| || ||||||||||||||||| | || || ||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||||
taatatgcaaacca-attttaaattcatgcagtcatcatggcaatgaataaaaatgtcgtattgatatgtatttaattactacatgtttcctttctatcagGTACATCCCATTACTAAAGGAGACATTTATGTTCCCACAAAGCTTGGGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGAT
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G410085_T01 (Zea mays), 3'ss of exon 4
tatcaattaaactatgttatgaacaaggacaacggtttggtctttctgctgacgattgattatagtac-taaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
|| | |||| | || | || || | | | | | | | | || || | || || | ||||||||||||||||| || ||||||||||||||||| | || || ||||||||||||||||| |||| ||| ||||| |||||||| |||||||||||||||||||||
taatatgcaaacca-attttaaattcatgcagtcatcatggcaatgaataaaaatgtcgtattgatatgtatttaattactacttgtttcctttctatcagGTACATCCCATTACTAAAGGAGACATTTATGTTCCCACAAAGCTTGGGCATTTTAGGTGTAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGAT
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173682_T01 (Zea mays), 3'ss of exon 4
--tatcaattaaactatgttatgaacaaggacaacggt--ttggtctttctgctgacgattgattatagtactaaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
| || | | | || || | | | | || | ||| || || || ||| | |||||| | | ||| ||||||||||||||||| || |||||||||||||| || | || || ||||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| ||
tgcagacatcatatcaatgaataaagatgccctataacaattaatgtttgtgttggtttatggatatgcaattaaccactgcatgtttc----ctttctatcagGTACATCCCATTACTAAAGGAGACGTTTAAGTTCCCACAAAGCTTGGGCATTTTAGGTGGAAAACCTGGGACGTCAACATACATTGCTGGGGTACAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctgacgattgattatagtactaaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
tactaac putative branch site (score: 0)
ctttctatc putative PPT
attgattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcaattaaactatgttatgaacaaggacaacggtttggtctttctgctgacgattgattatagtactaaccatttcctgtcattggactttctatcagGTACATTCCTTTACTAAAGGAGACATTGACATTTCCTCAAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA