ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacag

Basic information

species	Zea mays
transcript	GRMZM2G018697_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G018697_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 8

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagttt-atttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgc-accatgatt-----gattgattactttattaatgaatcgtgtaatgattttgtacag
|| | ||||| ||||| || ||||||||||| |||||  |||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||  | |||| |||| ||   | |  |   | |  |  ||  |   ||||  |||  |||    | ||   |    |   || ||| |        || |  | | | |||   | | ||||   || | ||| |||
TGCTAGATATTGAATGCTTCTCTTATCTTAATCGTGCTCTGGAGAGCCCATTATCACCAATTGTGATACTTGCGACAAATAGAGGAATATGTAATGTAAGgtaaacggtttgatttaccgctcgaagcactctgtcacattgcagtaccagagtaatactgcgtctatcagtttgtctattactatgctccttaaagttaacaagtcttttatatacttgtgt---gaatgtgtccag

upper sequence: GRMZM2G018697_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 8

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagttt-atttgccagacta--ctcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacag
|||| || || ||||| || ||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||||||  |||||| |||| |||| | |  | ||    ||||  ||  |   ||||  |||   |||  |||||   |   ||  |  |  ||    |  |||   | |||   | || ||| ||| || ||| |||
TGTTAGACATTGAATGCTTCTCTTATCTTAATCGTGCTTTGGAGAGCCCATTATCACCAATTGTGATACTTGCTACGAACAGAGGAATATGTAACGTAAGgtaaacagtttgatttaccagtcgaagcactctgcgctacattataataccagactaatcatgtgtttgtcagtttgttt--attaccatatgctccttaaagt-ttacaaagtcttgttatgcttgtgtccag

upper sequence: GRMZM2G018697_T04 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 8

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgta-ggcagtttatttgccagactactcttgcagctaagttcaatacccagcataaatctgtacttgtctactaagttgcaccatgattgattgattactttattaatgaatcgtgtaatgattttgtacag
|| ||||||| || |||||||| ||| | || |||||  | |||||| || | || ||||| || ||  | |||||||||||||||||||||||||||||||| |||| | ||  ||  | | |   |    | ||  |   ||||    | | ||||   ||| | |||  |      ||      ||  ||  || ||||   ||                         
TGCTGGATATGGAGTGTTTTTCATATTTGAATCGTGCTCTAGAGAGCTCACTGTCTCCAATAGTAATTTTCGCTACAAATAGGGGAATATGTAATGTAAGgtatggcattctacctgtgaaaatgaccaaataacttgg---aataggatgaaaaaat---tacctatcttttctaac-cattgcagtttttttttttcttttggaa-------------------------

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|60340836|gb|DN207809.1|DN207809

EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|22490622|gb|BU050545.1|BU050545

EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|61118430|gb|DN559391.1|DN559391

EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAAATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|87152471|gb|DY397260.1|DY397260

EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|61118429|gb|DN559390.1|DN559390

EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|31612365|gb|CD568987.1|CD568987

EST:     ATAGGGGAATATGTAATGTAAG                         AGGATCTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: ATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|31612366|gb|CD568988.1|CD568988

EST:     TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGNGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|213174323|gb|FM191608.1|FM191608

EST:     TTATCACCAATTGTGATACTTGCTACGAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCAGTGGATCTTCTAGATAG
genomic: TTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

EST: gi|149051700|gb|EE155813.2|EE155813

EST:     AAATAGGGGAATATGTAATGTAAG                         AGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG
genomic: AAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 174

TGTTGGATATCGAATGTTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATCGTGATACTTGCTACAAATAGGGGAATATGTAATGTAAGgtaggcagtt ... ttttgtacagAGGAACTGATATGACAAGTCCACATGGTATACCGGTGGATCTTCTAGATAGGCTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 69

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104