ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacag

Basic information

species	Zea mays
transcript	GRMZM2G004528_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004528_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 8

--ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttac-----aaaacctgaatgacag-----
    |       |  | | || | |    |  | ||||||| |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| || || ||    | |   |||||   | | | |       |      |  |      ||  | |  || || | ||  |       ||||   |  |    |     
TTGACTATGTTGTTGTTTCACTTGTTATCC--TGTGCAGGAGAAGTTCCATTCCTTCCATCCAGTGGCTACCATCCTGAGCTACCTCACCAAGGCACCCCTTgtgagtgcataca--tgcatctgtactgcccattaaccgttatgttctttcatgatataccaactgatttacttatgtcacgaaaaattcgtctcctggaacag

upper sequence: GRMZM2G004528_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 9

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttac-----aaaacctgaatgacag-----
                                     || |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| || || ||    | |   |||||   | | | |       |      |  |      ||  | |  || || | ||  |       ||||   |  |    |     
-------------------------------------GAGAAGTTCCATTCCTTCCATCCAGTGGCTACCATCCTGAGCTACCTCACCAAGGCACCCCTTGTGAGTGCATACA--TGCATCTgtactgcccattaaccgttatgttctttcatgatataccaactgatttacttatgtcacgaaaaattcgtctcctggaacag

upper sequence: GRMZM2G004528_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G14670.2 (Glycine max), 5'ss of exon 9

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagcct------tttcgcctgcattaattccg-gcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacag
                                     |  ||||||||||| |||||||| || || |||||||| || ||||| |||||||| || ||||||||  |      | |       | |  ||| | | ||   | || | |  |||     |||     |        |     ||||    | ||| ||||
-------------------------------------GGAAAGTTCCACTCATTCCACCCAGTTGCGACCATCCTCAGTTACCTGACCAAGGCCCCTCTGgtaagtataatgtatctgattcataattgttcagtgaattttttcatcccccctttgattaattttctcaaattgtgtgaacaacaattattaaattacag

upper sequence: GRMZM2G004528_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G31450.4 (Glycine max), 5'ss of exon 6

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgc-tccaatccagccgctaatcttctcttacaaaacc--tgaatgacag
                                     |  || |||||||| |||||||| || || ||||||||||| ||||| |||||||| || |||||||| ||  |       ||| ||    |  ||  || |     |||  | |     ||      |||  ||||   | | ||    | ||| ||||
-------------------------------------GGAAAATTCCACTCATTCCACCCAGTTGCGACCATCCTTAGTTACCTGACCAAGGCCCCTCTGgtaagtctaatactaccgattcataattgt-tcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaattacag

upper sequence: GRMZM2G004528_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 9

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttttcgcctgcatt----aattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctctt---acaaaacctgaatgacag
                                     |||||||| || ||||||||||| || ||||||||||| || |||||||||||||| || |||||||| || |   | ||||||    |  |      | | ||     |  | |  || | ||   ||  ||||| |   ||   ||   |   |||  ||| 
-------------------------------------GACAAGTTTCATTCCTTCCACCCAGTTGCCACCATCCTCAGTTACCTCACCAAGGCCCCTCTGgtaagtctctctacatgcatttcaaagctttaaacttggtgggtt-ccccatattctattctcccctttaatcgttgatttggacttgataagaaccacac

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|13515776|gb|BG518052.1|BG518052

EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG

EST: gi|78023487|gb|DV491874.1|DV491874

EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG

EST: gi|6021804|gb|AW066732.1|AW066732

EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCNCTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG

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: 152

ATCAGCACCATCATCTAACGTCTCTCTCATTATGCAGGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

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