ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgtgacatatttcctgtgttctcaacttctcatttcattagatgcattatgaaccacttgaatccttacccatgtaacattttatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT

Basic information

species	Zea mays
transcript	GRMZM2G108115_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 6

gtttgtgacatatttcctgtgttctcaacttctcatttcattagatgcattatgaaccacttgaatccttacccatgtaacattttatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
          | | | |    |  |||  || ||| ||||| | ||||| | ||    | |  ||  | || || || ||  || | || |  |||||||||||||| ||||||||||| |||||||| ||| | ||||||||||||||||||| |||||| || |||||| |||| ||||||||||||||||||
-------gtgtgtgttcatgttattcatgttttcagttcataatatgcact-tgtctgattcaaaatcatatccttggaatgttattttcac-agTGCAATTATGGATTGTGTTGGATGTGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G23150.2 (Glycine max), 3'ss of exon 7

gtttgtgacatatttcctgtgttctcaacttctcatttcatta--gatgcattatgaacc----acttgaatccttacccatgtaac---attttatttatt--agTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
       ||   |||    ||||||| | || | |||  | ||  ||| ||   |  ||     | ||   || ||  | ||| ||    ||||| |  | |  |||||| | ||||| ||||| ||||| ||||| || ||| | ||||| ||||| || |||| |||||||||||||||| | || ||||| ||||||||||||
------cactccttttacttgttctccatttattattctactactgattcaacttacacttttgatttatctcattggcaatggaatgttattttgtggaatgcagTGCATTGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGTAAGCTTCAGGTTCTTGGTCTTGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 7

--gtttgtgacatatttcctgtgttctcaacttctcatttcattagatgcattatgaaccacttgaatccttacccatgtaacattttattt----at-tagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
    |||      ||||  | |  |   |     |||  | |     |||  |       | ||   || ||  | ||| || || || |||    ||  |||||||| ||||| ||||| ||||| ||||| || ||| | ||||| || || || |||| |||||| ||||||||| | || ||||| ||||||||||||
ttacttgctctccatttattattctactactgattcaacttacacactgc--tgcttttgatttatctcattgacaatggaatatatttttttggaatgcagTGCAATGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGCAAACTTCAGGTTCTTGGTCTCGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7

-----gtttgtgacatatttcctgtgttctcaacttctcatttcattag-atgcatta--tgaaccacttgaatccttacc-catgtaacattttatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
       ||| | | | |  |   | ||||  |    | ||   |||   |   | ||  | |   |  |   |  |||   | || | | | ||   |   |||||||| ||||||||||| || || ||||| ||||| || ||||||||||| ||  |||  ||||| || |||||| |||||||||| ||| ||||  ||
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 7

--gtttgtgacatatttcctgtgttctcaacttctcatttcattagatgcattatg--aaccacttgaatccttacccatgtaacattt-tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
  | ||   |  ||     |  ||     |  | | ||||   |       || |    |     ||| | | |       | ||||||  ||||   |||||  | ||||||||||||||||| ||||||||||| || ||||||||||| ||  ||| ||||||||| |||||  | ||||| || ||||||||||||
aagcttcaaaagtacacattaagtggcttatctattattttggtgagccttttcttttgatagtgtgattacattaaataattacatttacattttgcagTGCCTTGATGGACTGTGTTGGATGTGAGAAGTGCCGGCTTTGGGGAAAGCTTCAGATTCTTGGTCTTGGCACTGCTTTAAAAATCCTCTTCTCTGTTGAT

upper sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7

---gtttgtgacatatttcc-tgtgttctcaacttctcatttcattagatgcattatgaaccacttgaatccttacccatgtaacattttatttatt--agTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT
    ||    |   |||||  |||| |||    ||        ||||  ||  |  |  |   ||       | |  ||  ||    | | || |||  |||||| | |||||||||||||| || |||||||| ||||| ||||||||||| || ||||||||||||||||||||| ||||||| ||||||||| |||||
aattttcactatgcatttcaatgtgatctttgattgctgcactattat-tgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT

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|32837058|gb|CD976736.1|CD976736

EST:     AATGGTCCTGAGCTTAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

EST: gi|37391024|gb|CF632751.1|CF632751

EST:     AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

EST: gi|149060175|gb|EE157145.2|EE157145

EST:     AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

EST: gi|31350402|gb|CD434759.1|CD434759

EST:     AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

EST: gi|31363348|gb|CD447705.1|CD447705

EST:     AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

EST: gi|24934189|gb|CA452407.1|CA452407

EST:     AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAG                         TGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT
genomic: AATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCT

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: 138

GATCTGCATGTCCATTGCCTTTTGATGAAGCCAAACTTTGGCAAGGCGAAAATGGTCCTGAGCTAAAGCAAGAGATTCAGAAGCAATTTAGAAACATTAGgtttgtgaca ... tatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttagatgcattatgaaccacttgaatccttacccatgtaacattttatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT