ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaacttgtactggtgcacttagactcattgagtcgctattgggctaattgtttaacttttacctgcag

Basic information

species	Zea mays
transcript	GRMZM2G173195_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G173195_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 5'ss of exon 4

AGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaa-------cttgt-actggtgcacttagactcattgagtcgctattgggctaattgtttaac---ttttacctgcag
|| | ||| |||||||||  |||||||||   ||||||  ||||||||| || ||||| ||||||||||| |||||||| || |||||  | |||||||||||||  |        ||||  ||| | |   |||    | |   |   ||  ||  ||| |  ||  |   ||| ||||||||
AGAGTAGCTTAAGCGTGACACATCCAGAAGTGAAGAAGCTTGTTGCTCCGGTCGAGCTGTGCCCAATACTAAAAACACTTTATAAAATCCTAATCAAGAGgttggtcagattacctttgttgctgttcctgctagtactaatatatgtgtacaggcttaagttctttgcacatttcacctgcag

Mapped 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|71321152|gb|DR797273.1|DR797273

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|113701733|gb|EE679237.1|EE679237

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACTACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|211410040|gb|FL464376.1|FL464376

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAA-TTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|148950857|gb|EC896476.2|EC896476

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|74237979|gb|DT645893.1|DT645893

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|148946890|gb|EC892170.2|EC892170

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|4966995|gb|AI691780.1|AI691780

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|211407489|gb|FL464375.1|FL464375

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

EST: gi|78023830|gb|DV492217.1|DV492217

EST:     GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAG                         GGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA
genomic: GTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTA

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 4 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

AGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTATGCCCAATACTCAAAACACTATACAAAATTTTGATCAAGAGgttggaaact ... ttacctgcagGGAGCTTACGACCAATTCCATCCTCCAGGCAATACGTGATGAATCAATGTATGATCCACGGGAAAGAATTGAGATGGCACAGAGGCAGTCTCTTTACCGG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 115

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67