Sequence
atgc intronic sequence ATGC exonic sequence...gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g33915.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------gccccatcgcgccacc-gcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG-------------------------
|| | | | || | || | | || | ||||||| | | ||||| | ||| || ||||||||| || ||||||||||| || || |||||||||| ||||| ||||||||||| ||||| |||||| | || |||
gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgggtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 2
---------------------------------gccccatc-gcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgt----tatgatacatg-----gttcctgt---tttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
| || | || | | ||| | || | || ||| || | | | || |||| ||||| | ||| || | | |||||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
gtaatgcagcatatctatttgattgtacttatacctttgtctgttttgatgctagcatgaatgtctgaaaatatctgcgaattctaaatgcctgttcagtgattaatgtgggatatgacaaatgagattgtatttatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009412_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------------------gccccatcgcgccacc-gcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
|| | | | || | || | | || | ||||||| | | ||||| | ||| || ||||||||| || ||||||||||| || || |||||||||| ||||| ||||||||||| ||||| |||||| | || |||
gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgggtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
---------------------------------gccccatc-gcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagca----gggtgcatttttcatgttatgatacatg-gttcctgtt-------ttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
| || | | | | ||| | || | || ||| || | | | || || | ||||| | ||| | | | || ||||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 2
gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatg-gttcctgtttt---cagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG----
| | | | | | | | || | ||||| || | | | || || | ||| |||| |||||||||||||||||||| |||| | |||||||||| | ||||||||| |||||| ||| | || |||
----------------gttcgttggttaaatatttcgttataagtgcataggaattaggatctttttttttttgctgacaaaaatatatttttatttaaaatagGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGGTTA
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 2
gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
| || | || | || | | | | | | | ||| | || | | | | || | | | |||| |||||||||||||| |||||| ||| ||| || |||||| | ||||||||| ||| |||||| | ||||||
------------------gtacaattctactgtttcccccaaacactgccttatggtt---tttattgctaataatttact-tttaattaat-taattagGCGAAAACCACCAAGAAAATTGTGTTGAGGCTCCAGTGCCAAGGATGCAAGCATGTCTCGCAGCACGCTATCAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 2
gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatg-gttcctgtttt---cagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
| | | | | | | | || | ||||| || | | | || || | ||| |||| |||||||||||||||||||| |||| | |||||||||| | ||||||||| |||||| ||| | || |||
----------------gttcgttggttaaatatttcgttataagtgcataggaattaggatctttttttttttgctgacaaaaatatatttttatttaaaatagGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
|| | | | | | ||| || | | | || | || | | || || | ||| | ||||| || || || |||||||||||||||| ||| |||||||||||||||||||||| ||| || | ||| || |||
gtatactcgcttttccttgtcttgatctctaattactgtcttctatgtgagaaccaatttaggatttcagaattgactctgtgaaatatgtcttataggaatgatttgttaattggaccttgc---tcattatttgtctttctttggaacagGCTAAGACAACTAAGAAGATTGTGCTGAGGCTTCAATGCCAAAGCTGCAAGCATTTCTCGCAACGCCCGATTAAG
upper sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------gccccatcgcgccaccgcgcacggcatt--------gttgctctcc-tccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
||| | | | | || ||||| | | | | | ||| | | ||| || | || | | | | |||||||||||||||||||||||| || |||| | |||||||||| ||||||| || |||||||| || ||||||
gtaacaatccatctatatccttatttccttggaaattttaaccctttttttaagttgtgtgatacttttctcagagattgctatttatatttttatatgccaaattttcata-acctttgattgcttttcacctaatcacc-taatcagGCAAAAACCACCAAGAAGATAGTACTGAGGTTGCAATGCCAGGGCTGCAAACACGTATCCCAGCATCCAATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
ttcctgttttc CT-rich tract
atttttcatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccccatcgcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC