ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag

Basic information

species	Zea mays
transcript	GRMZM2G114793_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctc--ctctgctgcctgaattctc-cattgtcagctg--cggga----ttggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
||||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || ||||||||||||||||| |  |        || |  |   ||| | ||  ||||     |||  | | |    |  |     |  ||||      | ||            |   |  ||
AGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAAGAAGTCCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagacataagcaaactttcttctttgagtcctgacattacatcctggtcagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtgg-tgtag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacg-gttactgctcc-tctgc--------------tgcctgaattctccat---tgtcagctgcgggattg--gt-agtaatgacctgtttgttttg----tcctgtaatccataaatacag
||||||||| |||||||| || || |||||||| ||||| |||||||| || ||||||||||||||||| |||||||||||||| || |||||||| ||||||  | |  | |  ||  | |||              ||| ||  ||     |   | | |  |||  || ||  || |   |||||  | |||  | |      |||   |   | |||||||
AGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCAACCAAGAAATCTCAGGTGTTCACCACCTATCAGGACCAGCAGACTACAGTCTCCATTCAGgtatggtgccattattcaatttgcattaaagggcatgatgcgtgtttttcttctaaatctaaaatgcatgactgtagtgaactatgacggggttgactcgaattcactgctttttcttaatacag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag---------------------
 || ||||| |||||||| || || |||||||| ||||| |||||||| || |||||||| |||||||||||||| |||||||  || |||||||| ||||||  | | | |  ||  ||||      |   | | ||  |||  ||     |   |   ||   | ||  ||| | ||   ||   |  |||  |  |                     
GGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAAGAAATCCCAGGTGTTTACCACCTACCAGGATCAGCAGAGTACCGTCTCCATTCAGgtatggctcattattcaactgc-attaaagggcacgatgctcaattgtcttctaaattcaaaatgcatgactgtgtagtgtagtggactttaataattgatgccttttctcaatacatag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgc-------tgcctgaa---ttctccattgtcagctgcgggattggta-----gtaatgacctgtttgttttgtcctgtaatccataaatacag--
 || ||||| |||||||| || || |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||| || |||||||| ||||||  | | | |      ||||       |||  ||    |  |    |   |  | |   |||  |      ||| ||  || ||  |  | |  ||   |   | ||||||   
GGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAAGAAATCTCAGGTGTTCACCACCTACCAGGATCAGCAGACTACCGTCTCCATTCAGgtatggctcattatctgactgcataaaagtgcacgatgcttgtttttcttctaaatccaaaattcatgactgtgtagtggact-ttaataatttgatgctttttctcaatacatag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgta-----------------acggttactgctcctctgctg---cctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
||||||||| |||||||| || || |||||||| |||||||||||||| || || ||||||||||||||||||||||||||||| || |||||||| ||||||                 | | |   || |  ||| ||    ||  ||| | ||| | || | ||    || | | | | |||| ||      ||  |   |  |   | |||||||
AGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAAGAAATCTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactat-gatgggattgacttgaaacgattcactgcttttttcttaatacag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
 || |||||||||||||| || ||||||||||| |||||||||||||| || || || ||||| || |||||||| ||||||||||| |||||||| |||||| |  | | |||    ||        | |||| ||   || | |  || |||| | |||||  |      ||| | |||| |    | |||   |||
GGTGATGACCAAGTTGATTCCTAGGAACACTGTTATCCCGACCAAGAAATCTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatc--tgaatgcaaacct--caatcaagttctacaagttctgttttggaattg-ttgtaatctcactggggttctctcctat----cttaacatcag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: EDP06660 (Chlamydomonas reinhardtii), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattc----tccattgtcagctgcg-ggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
 |||||||||||| |||||||  | |||||||||||||| |||||||||||||||   ||||| ||||||||||||||||||||||| || |||||||||||    |    ||   |   | ||    ||| |      |   ||||  |||  |||   |  |   | | || ||||    |    |        ||| |   
CGTCATGACCAAGCTGATCCCCCGCAACACTGTCATCCCCACCAAGAAGTCGCAGACCTTCACTACCTACCAGGACCAGCAGACCACCGTGTCCATCCAGgtgcgcgcgcatgaggcaacgatggggaaatgcagggcacggcgtcatgtgcaaggaaccggcgaggtcatctatttgg---ggggggggggtggcaaacaag-

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
||| ||||||||| ||||||| |||||||| ||||| |||||||||||||| ||||| |||||||| ||||||||||||||| |  | || ||||| || ||||  ||      |||     |  ||| ||  |  |        |||  | |||||| ||                                      
AGTGATGACCAAGCTGATCCCCAGGAACACGGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaa--gtcgtcattccctcttttgctgtatggtagagctaactttgctcggttggta-tag-------------------------------------

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag
||| ||||||||| ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||| |  | || ||||| || ||||  ||      |||     |   || ||||      ||    || || |  | ||    ||  | ||| || | |                     
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaa--gtcgtcattccctctttcagtgcattc------gtgctgtgtggtagagctaactttgctcggttggtatag---------------------

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|67021339|gb|CO450088.1|CO450088

EST:     CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggtta ... ataaatacagGTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG

EST: gi|5343005|gb|AI795310.1|AI795310

EST:     CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggtta ... ataaatacagGTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG

EST: gi|20803248|gb|BQ294298.1|BQ294298

EST:     CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggtta ... ataaatacagGTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAG

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: 142

AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggtta ... ataaatacagGTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTCAACGGCATTGCGCCAGCTCCAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128