ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag

Basic information

species	Zea mays
transcript	GRMZM2G052658_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g54510.2 (Oryza sativa), 5'ss of exon 6

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggat-cctgact-tgtcccaaactcaaatactctctgatcag
||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| |||||||| |||||||||||||| || |||||||| ||||| ||||||||||   ||| ||         ||| || |     |   ||| | ||| |||||| | | ||||||| |   || | |||    | | |||| ||||
TGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGTGAGAACCTACTGGTCAACATGAGGGATCCACAACGACCAATCTGCAAAgtttgatccctgccctctcat-------cttcatttcctcagctcttgct-tca-aatggttgttacctgactgtcatcccacctc---cattttctgctcag

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G01190.2 (Glycine max), 5'ss of exon 8

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccag--cctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| ||||||||||||||||| || || || || ||||||||  ||||||||||||||||| |||| || ||||| ||||| || || || || ||||||||         |   | |   | |   ||| |  |       |  ||  |    |    | | |||   |||  ||    | | |    || | | | |    
TGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacatacacatacactgatgcagacaaaagccaaaagcaacc-tgctagcggagattgaaatg----agatttgtgtaatttttcag---

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G07320.1 (Glycine max), 5'ss of exon 11

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccag--cctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| ||||||||||||||||| || || || || ||||||||  ||||||||||||||||| |||| || ||||| ||||| || || || || ||||||||         |   | ||  | | | |||    | |       |||       |    | | |||   |||  ||    | | |    || | | | |    
TGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGTGAGAATCTATTGGTCAATATGAGAGATCCTCAACGGCCTATCTGCAAGgtacacataagaatacattcacatatactgaggcaacaaaagccaaac--gcaacctgctagcggagattgaaatg----agatttgtgtaatttttcag---

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 5'ss of exon 6

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| |||||||||||||| || ||||| || || ||||| ||  |||| ||||||||||| || ||||||||||| ||||| ||||| || || |||||||||   |    |  | |    ||| ||  | || |     | ||  |  | |     |  |  ||  || |||        ||   |              
TGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGTGAGAATCTTCTTGTGAACATGAGAGATCCTCAGCGTCCTATATGCAAGgttctgttgttactcatctgatct-ctcatataacaaagagtaagcttatatgtttctcataaattttgtctttctttttccttccag-------------

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 5'ss of exon 5

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| ||||||||||| ||||| |||||||| || ||||||||| | |||||||||||| || | || || ||||| ||||| || || ||  |||||||||| || |    |    ||     |  |  ||| |     |       |     |   | ||| ||  ||   |  ||     |||  |   ||   |  ||
TGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGTGAGAATTTATTAGTAAATATGAGAGATCCACATCGGCCTGTTTGCAAGgtatgtttgtta-taattataaatattaatttttgagcttttctgcggcacctaatcttgtgaattatgttattcccttccatcatttgtcctagaactag

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ30928 (Selaginella moellendorffii), 5'ss of exon 3

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccccagcctttccctctgctgctttatctttctggaaattgttgt-cacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| ||||||||| | || || ||||| || || ||||| |||||||| || |||||| | ||||| |||||||||||||| || || ||| | ||||||||   |     | | |   |    | |  || |  ||   |  | |   ||| |||  |    |                                      
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgt---aatgatatcttcgtctctcgttctttcactttgtagtgagtgactgtgcacgtttccag--------------------------------------

upper sequence: GRMZM2G052658_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ17246 (Selaginella moellendorffii), 5'ss of exon 3

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtt-tgat-ccccagcctttccctctgctgctttatctttctggaaattgttgtcacaatggtggatcctgacttgtcccaaactcaaatactctctgatcag
||| ||||||||| | || || ||||| || || ||||| |||||||| || |||||| | ||||| |||||||||||||| || || ||| | ||||||||  ||||  |   | || ||  |||   ||||| |  |    |  | |||   |||  |    |                                      
TGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCGAGAATTTGCTGGTCAACATGAGGGATCCACATCGGCCAGTGTGCAAGgtaatgatatcttcgtctctcgttctttcgctttgtagtg--agtgactgtg--cacgtttccag--------------------------------------

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|24764857|gb|CA400019.1|CA400019

EST:     GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATCTGCAAG                         ATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGT
genomic: GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccc ... ctctgatcagATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGT

EST: gi|211480675|gb|FL225292.1|FL225292

EST:     GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAG                         ATCGGTGATCTTGGACT
genomic: GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccc ... ctctgatcagATCGGTGATCTTGGACT

EST: gi|211480678|gb|FL225295.1|FL225295

EST:     TGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAAG                         ATCGGTGATCTTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTG
genomic: TGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAA-Ggtttgatccc ... ctctgatcagATCGGTGATCTT-GGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTG

EST: gi|74237122|gb|DT645036.1|DT645036

EST:     GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAG                         ATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGT
genomic: GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccc ... ctctgatcagATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGT

EST: gi|116814956|gb|EC857584.1|EC857584

EST:     GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAG                         ATCGGTGATCTTGGACTGTCAAAGGTTAAACAACATACTTTGGTATCTGGT
genomic: GTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccc ... ctctgatcagATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGT

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: 46

TGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGTGAGAATCTACTGGTGAACATGAGGGATCCGCAGCGACCAATTTGCAAGgtttgatccc ... ctctgatcagATCGGTGATCTTGGACTGTCAAAGGTTAAACAGCATACTTTGGTATCTGGTGGTGTTAGAGGAACCTTACCATGGATGGCACCAGAGCTTCTGAGTGGGA

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 30

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66