ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtag

Basic information

species	Zea mays
transcript	GRMZM2G068392_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtag
||| ||||||||||| |||||| | ||||||||||||||||||||| |||||||||| ||||||||||| ||||||| |||||| |||||||||||||||||||||||||||  ||||||||       |  | |||| ||||||| ||  | ||   | ||   ||| |    ||| ||| |  | ||  ||||   |     |   |||     |    | || ||||||| ||||| || |  ||
TGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTgtatggagtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacag

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtag
       |||||||| |||||| | ||||||||||||||||||||| |||||||||| ||||||||||| ||||||| |||||| |||||||||||||||||||||||||||  ||||||||       |  | |||| ||||||| ||  | ||   | ||   ||| |    ||| ||| |  | ||  ||||   |     |   |||     |    | || ||||||| ||||| || |  ||
-------CTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTGTATGGAgtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacag

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G00430.2 (Glycine max), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttt-tttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtt--tgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtag
||| ||| ||||  | || ||||||||| | ||||||||||||||||| ||||| || ||||||| ||| ||    | ||| || || ||  ||||||  |||   ||||     |||     | |  || |   ||   |  | | || | |     || |  | || |     |||||  | |  | ||     ||| ||                                      
TGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGTTCAAAAATGACCCTGACGAGGAAAATGAAgta---agtacatccttgcaaactctctcccacccctctttctctttcagtttcaaaatgcttactgagggccatatgttgatacaatggttccatctacata-------------------------------------

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G36520.1 (Glycine max), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctg-cattgtacttctgatagccgaagctttcatgtt--tgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtag
||| ||| ||||  | || ||||||||||| ||||||||||||||||| ||||| || ||||||| ||| ||    | ||| || || ||  ||||||| |||   ||||     |||  |  | |  |     | | || | ||  || | |     || | || || |     |||||  | |  |  |     ||| ||                                      
TGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGTTCAAAAATGACCCTGACGAGGAAAATGCAgta---agtacatccttgcatgctctctcctacccatcgttctctttcagtttcaaaatgcttgctgagggccatatgttgatacaatgtttccatctacata-------------------------------------

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagt-----cattactatatcttctgtatcg--tgatcttgctattcggaacccttgtag
 || ||| ||||| |||| || |||||||||||||||||||||||  | ||||||||  | ||||   | ||    | ||| |||||| |   |||||| ||| | | |  |   ||| |  | | ||||  || ||  |    |   ||||||   |  |   | |    ||   |||   ||| |      ||  ||||  ||| ||   | |  | |   ||  |||   |    | | ||
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtactt-gtccttgctaatgt-accatttttttcttattttat-ttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttat-gcag

upper sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 5'ss of exon 6

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtag
||| ||| ||||| | || ||||||||||| ||||||||||||||| ||||||| || || |||| ||||||    | ||| || |||||  ||||||| || | |   | ||||||  | |   | | || || ||      |||         | ||||||  ||||| |  |  | || ||   | || |  |||| || |  |||    || |                    
TGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTATTCAAAAATGACCCTGATGAGGAAAATGCGgt-tagtaaatgagatttctgtgcattcaaaatttttgaacttctga--------tttgatagt-gaagcct--acttctggttgtcttat-agcatattttgtccatc----tcct--------------------

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|211178282|gb|FL421437.1|FL421437

EST:     TGATCCGGATGATAAAAATGCT                         GAATTCGCGTAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: TGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG

EST: gi|78076513|gb|DV504947.1|DV504947

EST:     AGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: AGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG

EST: gi|60342736|gb|DN209709.1|DN209709

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg

EST: gi|60342736|gb|DN209709.1|DN209709

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg

EST: gi|60342736|gb|DN209709.1|DN209709

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg

EST: gi|60342736|gb|DN209709.1|DN209709

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg

EST: gi|71433967|gb|DR815017.1|DR815017

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG

EST: gi|50324142|gb|CO519268.1|CO519268

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAA
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAA

EST: gi|38502614|gb|CF972474.1|CF972474

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCCCGGAAGCGGATTCATTCTTTTGCTTCGCCGAGTTGCTTA
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTA

EST: gi|50331308|gb|CO526434.1|CO526434

EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GTATGGAGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCT
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagG-A---A---TTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCT

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: 127

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

RNA-Seq data