ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataacattttctttcatgttgtgtgttgtcttcccatcctctcttgttattcaacttatactgatgacaggcattgttgtacag

Basic information

species	Zea mays
transcript	GRMZM2G109039_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G109039_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 5

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataacattttctttcatgttgtgtg-----ttgtcttcccatcctctcttgttattcaacttatactgatgacaggcattgttgt----acag
  ||||  || | || |||| |||  ||| ||| ||||| ||| |||||||| | ||||| || ||||| || |||||||||||||||||||| |||||||||   || | | || ||   ||||   |      || | | | |  | |||    ||  |  | |  || |||||       || || |    ||||
TGTCTATTTAATGTCACATTTCTCTGTTCTTCATTGGTCGGCACTGAGTGGTCTTGATACCGAGCTTATGAATGTCCAAGGACATGTGGCACCCAGGGAGgtatggtaccttctttttctttgttccatcaatttttatttactctgcttctaagttttatgtattagtattgatgtttcatgtttttcttattacag

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|58029875|gb|CX725302.1|CX725302

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|60347828|gb|DN214801.1|DN214801

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|8368895|gb|BE051840.1|BE051840

EST:     AAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: AAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|20301188|gb|BQ164131.1|BQ164131

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|453303|gb|T15277.1|T15277

EST:     GTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|67012835|gb|CO441584.1|CO441584

EST:     TGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTAC
genomic: TGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAA-GGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTAC

EST: gi|20301181|gb|BQ164124.1|BQ164124

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|20300911|gb|BQ163854.1|BQ163854

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|20301275|gb|BQ164218.1|BQ164218

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCATGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|20300918|gb|BQ163861.1|BQ163861

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

EST: gi|26456084|gb|CA827667.1|CA827667

EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

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: 49 (upstream exon), 49 (downstream exon)
Score: 519

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 789

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 892