Sequence
atgc intronic sequence ATGC exonic sequencegtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g03760.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 7
gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagctt-gaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
|||| ||||| || || |||| || | |||| | || ||| | | || | ||| ||||| ||| |||| ||||||||||||||||||||| || ||||||||||| |||||||| || || ||||||||||||||||| |||||||| || ||||| ||||||| |||||
gtat-cttctgatc-ttccattcttgtcaacttatgctgctgagccgaacaaattcaattaatcttctgatttatgtaccagGTCTGCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 9
gtatatttc---tgttcat--tacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
|||| || | |||| | || | || | |||| | | |||||| | | | ||| |||| ||| |||| |||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||||||||||||||| |||||||| ||||||||| | |||||||||||
gtatcttctgaattctcatcttccagtcttgtcaacttatggtgctgatgagaacaatccaattaatcttctaatttgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
--------------------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatat------tctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
| | || ||| | || | | | | || |||| || || | |||| | |||| | | || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| | |||||||| || ||| | |||| ||||| ||
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 8
--------------------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatat------tctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
| | || ||| | || | | | | || |||| || || | |||| | |||| | | || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| | |||||||| || ||| | |||||||||| ||
gtatgttggaaagctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgtaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtatatt--tctgttcattacattgttctgaactcgtcctattgatgacagtagcttgacca-atattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
||||| | | | ||||| ||| | || | || | || | ||| | | || | |||| | | || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| | |||||||| || ||| | |||||||||| ||
gtatgttggaaaactcaggctatttttctttccttcagttatgtataataattgatacattatattatatgtaat--attctttcaattaatctagatgatatatgtaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
--------gtatatttctgttcattacattgttctgaactcgtcct--attgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
|| ||| | | ||| ||| | | || || | || | | | || ||| |||||| | || |||||||||||||| |||||||||||||| || || | || || || ||||||| |||||||||||||||||| | || ||||| ||
gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacg-tgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctg---tattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
| | | || || ||| |||||| ||| | || | | || | || | |||||| | ||||||| ||||| || ||||||||||| |||||||||||||||||||| | || || |||||||||| ||||||||| |||||||| | || ||||| ||
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacc--tggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTACMapped 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|58684950|gb|CK073637.1|CK073637EST: TTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGATGGTGTTTGGG GTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
genomic: TTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGATGGTGTTTGGGgtatatttct ... tctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
EST:
gi|55827892|gb|AU063117.2|AU063117EST: GTAAAATTGGATGGTGTTTGGG GTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
genomic: GTAAAATTGGATGGTGTTTGGGgtatatttct ... tctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
ttctgttttct CT-rich tract
aatattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG