Sequence
atgc intronic sequence ATGC exonic sequencegtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g39570.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 1
-------------------------gtgagttatc-caatgccgttctcc-gcctgaattcgttc----cgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttgggggggg-----ggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
|| | | | |||| || | ||| ||| || | || ||||| ||| || | | ||| | | || || | || | | | |||| ||| | | || ||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| ||||||
gtaagcgctcccctccccttgcccgccgaacttccgcctcttcgttttcttaattaaatctcttcgcggcgcgcgggactcgtgttgtttgtgcgcgcgccgccctttctgtttctgtttctgttttcttcttctggtgaggctgggtcgggtctctgagtggcgccaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
|| || ||| | || ||||| ||| || | || | | | | || || | | | | || | | | || | | | | ||| || ||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||| ||||||
gtaagcacccca----ccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttccttt-------ttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
| || ||| || | |||| | ||| || || || || ||||| || || ||| | | || ||| |||| || || || | |||||||||| ||||| |||||||| || |||||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||| ||||||
gcacgtcttcctattctgttccct-------ttcactcagtcctctgcgtc-----cggttagttactgttctgttccgat---tcgttactaattgatgattactaccatt-----------------gacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
| || ||| || || ||| | | | | | | ||| | || ||| | ||| | || | |||||| | |||| || || ||| |||||||||| || || |||||||| || |||||||||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||| ||||||
gcacgtcctcctattcccttccct--ttcactcctctgcgtccga----ttagttactgttctattctgctccgattcatt--------actaattgatgattactattgac--------------------aatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC
attgtatttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG