Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaggccttttgaattttctattagcctctggatttcactgttcatgttttatttttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56580.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 7
gtaagcaggccttttgaattttctattagcct--ctggatttcactgttcatgttttatttttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
|||| || ||| | |||| ||| ||| || || | || | |||||| | || || | |||||| ||||||||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||||||| ||||||||||||| ||||
gtaactagtatatttactgagtttatttgccatactgtatctcccgattatttatttatt--ggtaattttctgtcagGTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 7
--------------------------gtaagcaggccttttgaattttctattagcctc---tggatttcactgttcatgttttatttttggaac-------attttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
| ||||| ||| | ||| | ||| | | |||| | ||||||| || ||| ||| | ||||| || ||||||||||| ||||| ||||| ||| | ||||| |||||||||||| |||| || ||||| | | | | ||||||||||| | |
gtaaacccttgtgatagttttttcaatcctgtcaacctttaacattaccatttattttggcatggttgtgactgactaatttttattaatgaaactcgtatcattgaattagGTTTGTGCATGGAGATGTGAAACCTGAAAACTTTTTGCTTGGTCAACCTGGATCAGCTGAAGATAAGAAGTTATATCTTATTGATCTTGGTCTGG
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------gtaagcaggccttttgaattttctatta---------gcctctg--gatttcactgttcatgttttatt--tttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
| || | || | ||| | | ||| || || | ||||| |||| || || || |||| || ||||| || ||||||||||| ||||||||||| ||| | ||||| || |||||| || | || ||||||||||| | | || |||||||| |||
gttagtgcgaatttttgttgtcgccaataaatccatctatttcgaacaaaaatatttacatttgcaccaaaaaattacgccattgctgagctgactgt-catgcattgttcattccctacatcaaacaagGTTTGTGCATGGAGATGTGAAACCAGAAAACTTTTTGCTTGGTCAGCCTGGAACAGCAGACGAGAAGAAACTATACCTTATCGATCTTGGTCTAG
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------gtaagcaggcctttt----gaattttct----attagcctctggatttcactgttcat-gttttatttttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
| | | | || | | | |||| | | || ||| ||| | | || || | ||||| | | | ||||| || ||||||||||| || ||||| || ||| ||||||| ||||||||| | ||||||||||||| || ||| | ||||||||||| || |
gtgagtactattaataattccatgtttcactttctcagaatcatcctgtctctcttgagcactttcctcaaagtggcttcttcattctgttaattattgtcatcttttttcttcctcaaccaagGTTTGTGCATGGAGATGTGAAGCCAGAGAACTTTTTACTTGGTCAACCTGGAACTGCTGATGAGAAGAAGCTATTTCTTATTGATCTTGGTTTGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29629024|gb|CB634035.1|CB634035EST: TGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGG GTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGG
genomic: TGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGGgtaagcaggc ... attttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGG
EST:
gi|29623307|gb|CB628318.1|CB628318EST: TGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGG GTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGG
genomic: TGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGGgtaagcaggc ... attttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctattagcctctggatttcactgttcatgttttatttttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
ttttacc CT-rich tract
ttttatttttggaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaggccttttgaattttctattagcctctggatttcactgttcatgttttatttttggaacattttaccagGTTCGTTCATGGAGATGTTAAACCAGAAAATTTTCTACTTGGCCAACCTGGATCACCTGATGAGAAGAAACTTTTTTTGATTGATCTTGGCTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA