ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgccatttatttttgcctggtagtctatatgtttctttgagacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcag

Basic information

species	Zea mays
transcript	GRMZM2G416120_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 7

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgccatttatttttgcctggtagtctatatgtttctttgagacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcag
 ||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||| |||||  |||||||| ||||  |||||||||||||||||    ||||  ||    || | ||  |||||||   ||    | |||||   |||  ||  |||||   | |   |   |               
TAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGAAATGTgtaagtt---tttaacttctgttgttggttgatatgttcagttttt-cttttggaactatctaagtcatgaggttatatttaacag--------------

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 6

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgccatttatttttgcctggtagtctatatgtttctttgagacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcag
||| ||| | | ||||||||| |||||||| |||||||||||  ||||||| || |||||||| ||||||||||| || ||| | ||| | || |||||||||||     |      |||     |  || || |      ||| |   ||   |||     ||   ||   | |   ||                    
CAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAAAATGTgtaaggat--tcccaccttgttactttatcaatttaaggaattgcggatttaatttgctctgaatgaatatgtgttgcag--------------------

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 7

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAAT------GTgtaagtgccatttatttttgcctggtagtctata--------------tgtttctttgagacctttggttgtata-----caacacatgaatatcttagttgtactttttgtatcgcag--------------------------------------------------------------------
 || || || | ||||||| | || ||||||||||||||||| || |||||||| || |||||||| || ||||| ||||| || ||  | || |||       || | |    ||||   |||||| || || |  |                ||| |  |  |  |  || ||| |  |     ||     ||    | ||| | || |||||  | |                                                                         
AAAAACTCTGTTTAATGAGTTGGAGGTTGTGGAGGGTATGAAGCTCGACAGAGGATATATCTCTCCCTATTTCATCACCAATTCTAAGACTCAAAAAGTGgttggtattaaaatcattatattttgcttgctacttcacggtagtcactgcagttgtgttatccatgctctttgttattcattcgtcattgagtgttctttttattcgtgcttttgattttttttgtctttctggatttagaagagcccacacttatatttgacgtcgtgttggtcgtttaccaatgatacag

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|50328354|gb|CO523480.1|CO523480

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

EST: gi|71425566|gb|DR806758.1|DR806758

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

EST: gi|149073906|gb|EE162234.2|EE162234

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCCAT-GATCTTAATTCATGACAAGAAAGTGACAAATAT
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCC-ATTGATCTTAATTCATGACAAGAAAGTGACAAATAT

EST: gi|78078492|gb|DV506905.1|DV506905

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

EST: gi|67019174|gb|CO447923.1|CO447923

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

EST: gi|149077207|gb|EE165873.2|EE165873

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTT
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTT

EST: gi|71425565|gb|DR806757.1|DR806757

EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

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: 653

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244