Sequence
atgc intronic sequence ATGC exonic sequencegtacgttggttcaatcggcggcgcgcgcgtggaactcattctggatcgagcggttttggtttgatatatatgatcgatttcgctgggcgtctcgatcgggtgctcacgcttggttattttctcgctttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G416965_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g08490.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------gtacgttggttcaatcggcggcgcgcgcgt----ggaactcattctggatcgagcggttttgg--tttgatatatatgatcgatttcgctgggcgtctcgatcgggtgctcacgcttggttattttctcgctttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT-----------------------------------
| | | | ||| ||| || | | | | |||| | || | || || || | | | | | || || ||| || | ||||| | || ||| ||| | | ||| ||| ||| | | | | | || | |
gtgtcccggacttgatccgcaacgtggtgggcatcgtcggcaatgtcatctcctttggcctcttcctctcgccggtgcccaccttctggcggatcatcaagaataaggacgtgcgggacttcaaggcggaccagt-acctagccacgctgctcaattgcatgctctagGTTTTCTATGGTCTTCCCATCGTTCACCCCAACAGCATTCTCGTCGTCACCATCAACGGTATTGGCCTCGTCATCGAGGCCGTCTACCTCACCATCTTCTMapped 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|211351800|gb|FK980889.1|FK980889EST: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCG GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT
genomic: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
EST:
gi|211351797|gb|FK980886.1|FK980886EST: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCG GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT
genomic: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
EST:
gi|149079042|gb|EE167926.2|EE167926EST: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCG GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
genomic: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
EST:
gi|211351796|gb|FK980885.1|FK980885EST: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCG GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT
genomic: ACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
EST:
gi|211351798|gb|FK980887.1|FK980887EST: GATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCG GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT
genomic: GATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 2 RNA-Seq libraries.
Block sizes:
23 (upstream exon),
27 (downstream exon)
Score:
2AAAGCCCCGCAGCTCTCGCATCTCATCAGACGCCACCACCACCTCCGGCGACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
Block sizes:
49 (upstream exon),
38 (downstream exon)
Score:
366AAAGCCCCGCAGCTCTCGCATCTCATCAGACGCCACCACCACCTCCGGCGACCGAAGATGATCTCTCCGGATGCAGCCCGCAACGTCGTAGGCATCATCGgtacgttggt ... ttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgggcgtctcgatcgggtgctcacgcttggttattttctcgctttggttgcagGCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT
tgctcac putative branch site (score: 366)
ttattttctcgcttt putative PPT
ttattttct TA-rich tract