Sequence
atgc intronic sequence ATGC exonic sequence...tttacagacatcattttctacttctgtgatatcactgctgccatgtatctggctatctgcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g45400.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G828278_T01 (Zea mays), 3'ss of exon 5
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggctatct---gcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| | || | |||| || ||| | | || |||| | ||| |||||| || ||| ||||||||||| | |||||||||||||||||||||||||| ||||| || |||||||||||||| ||||||||||| ||| |||| | ||| | |||||| ||||
-----gaatgatgttttttactttgttatgctggtgctgcagcaatgagctcagtttgcttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGCGTTCATTGTCTGAGCACGTTCCTCATGGTTACCGTAGGAAATCACTTTTTGAAGGTCTAATTCGATATAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G412814_T01 (Zea mays), 3'ss of exon 4
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggctatct---gcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| | || | |||| || ||| ||| || |||| | ||| |||||| || ||| ||||||||||| | |||||||||||||||||| ||||||| ||||| || |||||||||||||| ||||||||||| ||| |||| | ||| | |||||| ||||
-----gaatgatgttttttactttgttatgctggtgctgcagcaatgagctcagcttgcttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGTGTTCATTGTCTGATCACGTTCCTCATGGTTACCGTAGGAAATCACTTTTTGAAGGTCTAATTCGATATAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G412814_T01 (Zea mays), 3'ss of exon 6
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggctatct---gcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| | || | |||| || ||| ||| || |||| | ||| |||||| || ||| ||||||||||| | |||||||||||||||||| ||||||| ||||| || |||||||||||||| ||||||||||| ||| |||| |
-----gaatgatgttttttactttgttatgctggtgctgcagcaatgagctcagcttgcttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGTGTTCATTGTCTGATCACGTTCCTCATGGTTACCGTAGGAAATCACTTTTTGAAG------------------
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114459_T01 (Zea mays), 3'ss of exon 7
tttacagacatcattttctacttctgtgatatcactgctgccatgtatctggctatctgcccattttaa-ctttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
||| || | || | ||| | || | | | | || | | | | || || || |||||| || ||| ||||||||||| | |||||||||||||||||||||||||| ||||| || |||||||||||||||||||||||||| ||| |||| | ||||| |||||| ||||
tttccattcctcgatc-ctatcaattcagtaatctgattactaaggctcagcttgcttacatgaagtagtctcctttcttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGCGTTCATTGTCTGAGCACGTTCCTCATGGTTATCGTAGGAAATCACTTTTTGAAGGTCTCATTCGATATAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036593_T01 (Zea mays), 3'ss of exon 2
tttacagacatcattttctacttctgtgatatcactgctgccatgtatctggct-atctgcccattttaacttt--ttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| | || | |||| | | || | |||| || ||| | | | | | ||| ||| || |||||| || ||| ||||||||||| | |||||||||||||||||| ||||||| ||||| || |||||||||||||| ||||||||||| ||| |||| | ||| | |||||| ||||
-tgaatgatgt--ttttactttgttatgctggtgctgcagcaatgagctcagtttgtttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGTGTTCATTGTCTGAGCACGTTCCTCATGGTTACCGTAGGAAATCACTTTTTGAAGGTCTAATTCGATATAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G806059_T01 (Zea mays), 3'ss of exon 2
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggct-atctgcccattttaacttt--ttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| | || | ||||| | || | |||| || ||| | | | | ||| ||| || |||||| || ||| ||||||||||| | |||||||||||||||||| ||||||| ||||| || ||||||||| |||| |
-----gaatgttgttgtttactttgttatgctggtgctgcagcaatgagctcagtttgcttacattcattagttttatttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGTGTTCATTGTCTGAGCACGTTCCTCATTGTTACC---------------------------------------
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G369559_T01 (Zea mays), 3'ss of exon 2
tttacagacatcattttctacttctgtgatatcactgctgccatgtatctggcta-tctgcccattttaact------ttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAA-GCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| ||| || |||||| || | | | ||| | || | | ||| |||||| || ||| ||||||||||| | ||||||||||| ||||||| ||||||| ||||| || ||||||||||||| ||||| ||||| ||| |||| | ||| | |||||| |||
------aatgatgttttttactt-tgttatgctggtgctgcagcaaatgagctcagtttgcttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAAGCGACTGTGTTCATTGTCTGAGCACATTCCTCATGGTTACCGTAGAAAATCACTTTTTGAAGGTCTAATTCGATATAAT-
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G087658_T01 (Zea mays), 3'ss of exon 3
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggct-atctgcccattttaacttt--ttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| | || | |||| || ||| | | | | | ||| ||| || |||||| || ||| ||||||||||| | ||||||||||||||||| ||||||| ||||| || |||||||||||||| | ||||||||| ||| |||| | ||| | |||||| ||||
-----gaatgatgttttttactttgttatgctggtgctgcagcaatgagctcagtttgtttacattcattagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTATGTTCATTGTCTGAGCACGTTCCTCATGGTTACCATAGGAAATCACTTTTTGAAGGTCTAATTCGATATAATG
upper sequence: LOC_Os07g45400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G326151_T01 (Zea mays), 3'ss of exon 2
tttacagacatcattttctacttc--tgtgatatcactgctgccatgtatctggct-atctgcccattttaacttt--ttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
| |||| ||||| | || | |||| || ||| | | | | ||| ||| || |||||| || ||| ||||||||||| | |||||||||||||||||| ||||||| ||||| || |||||||||||||| ||||||||||| ||| |||| |
-----gaatgatgttttttactttgttatgctggtgctgcagcaatgagctcagtttgcttacattcgttagttttctttctttacatccattattgccttgcagGCCCTTGCTCAGCCAAACAAGCGACTGTGTTCATTGTCTGAGCACGTTCCTCATGGTTACCGTAGGAAATCACTTTTTGAAG------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctggctatctgcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
attttaactttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttacagacatcattttctacttctgtgatatcactgctgccatgtatctggctatctgcccattttaactttttgattacatgtgccatcgccatgcagGCCCTTTCCCAGCCAAACAAGCGACTGCGTTCATTATCTGAACATGTTCCTCATGGTTATCGTAGGAAATCTCTTCTTGATGTTCTCACTCGATACAATG
- -acagaca
- - - - - - - - - -acttctg
- - - - - - - - - - - - - - - - - -tgctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc