ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagccctgcacgatacttccagctcttggcacatttgtttgcgtactgtaaaactgactgtacttggtaacatgttcttgcag

Basic information

species	Zea mays
transcript	GRMZM5G836588_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 5'ss of exon 13

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagccctgcacgatacttccagctcttggcacatttgtttgcgtactgtaaaactg-actgtacttggtaacatgttcttgcag
|| |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| |||||||||||| ||||  || | | | |||| | ||||||||||        | ||  ||||        || ||    || ||| ||| |||
GTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCAgtaagta-ccctttac-acaatgccagattttggcacattgccacagttgctagaaaatcatgtaatatttatgtacttgtacttacag

upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA01G06730.1 (Glycine max), 5'ss of exon 15

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgt-------aagtagccctgcacgatacttccagctcttggcacatttgtttgcg--tactgtaaaactgac-tgtact-tggtaacatgttcttgcag--------------------------------------------------------------------------------------
|| ||||||||||| |||||||| ||||| ||  | ||||| |||||||||||||| || || ||| | || || || || ||||| |||||||       | ||   | ||    ||| ||  |    || |  | |||   |     || |  |  | | ||    ||| ||||   |  || ||| |                                                                                       
GTTTGGAAGAAAGTGGTATATGTTGATAGACTACTCCAGCTCTTCAGATATGTACCCCGTGAACAATTGACCATCCCAGATTTTGTCTTTCAgttgagtctatgttttcatgtgttatatttataatcatttgttccttttcataatgctattacatgagtaacacacactctggtttaaatttattggaaattacaattaaataaaaagcgagacttagaagtaaatgtactttagattataggttctaattcattttgtacttttattctcaaag

upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA20G03330.1 (Glycine max), 5'ss of exon 14

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgt-aagtagccctg------cacgatacttccagctc-ttggcacatttgt--ttgcgtactgtaaaactgactgtacttggtaacatgttcttgcag--
|| ||||||||||| |||||||| ||| | ||| ||||||| |||||||| ||||| || || ||  | || || || || ||||| |||||||  |||     ||      ||| || |   ||   | ||  |   ||  |  |    | ||||  ||    |  |  |   ||    | |  || |   
GTTTGGAAGAAAGTGGTATATGTTGATCGCCTTCTGCAGCTCTTCAGATACGTACCTCGTGAACAGTTGACCATCCCAGATTTTGTGTTTCAgttgagtgtttatgttttcacacaatgccatcaatacgttttctttttcataatattattctgtgcaatgtgccattttcaatatacggcttctgaaaag

upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 5'ss of exon 14

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagta-gccctgcacgatacttccagctcttggcacatttgtttgcgtactgtaaaactgactgtacttggtaacatgttcttgcag
|| |||||||||||||||||||  ||  | ||| |||||||||||| ||| || || || ||||| || ||||| || ||||||||||| ||||||||   | || | |   ||   |   |   |  |  |  |||  ||   |||   ||| |||  || | ||         ||||||
GTATGGAAGAAAGTTGTATATGCAGACCGACTTCTGCAGCTGTTCAAATACGTTCCTCGTGAGCAGCTGACAATCCCAGACTTTGTTTTCCAgtaagttcactctactcctcacactctagtaacgttat-tcagttctcgatttgttttacttactagaccttgtg-tgaaaaattgcag

upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 5'ss of exon 13

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagccctgcacgatacttccagctcttggcacatttgtttgcgtactgtaaaactgact-gtacttggta-acatgttcttgcag--------------
|| ||||||||||| |||||||| ||  | ||  |||||||||||||||| || ||||| |||||  | ||||| || |||||||| |||||||    ||   |      |  ||| |  ||| | |   ||   |    ||     || |    | |||   |    |||| |  ||  |               
GTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCAgttg--agttttctgttctttttcaaaatctggacttgttc--tcaattatcaataaccaagttagtaaccgtcccacatctaattaaaaggcattcctgatag

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|211406752|gb|FL443984.1|FL443984

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|211075806|gb|FL464165.1|FL464165

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|4621446|gb|AI612279.1|AI612279

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|148929297|gb|EC875052.2|EC875052

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|78125404|gb|DV543788.1|DV543788

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGTTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|94478486|gb|EB707444.1|EB707444

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|211124589|gb|FL474104.1|FL474104

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

EST: gi|76286117|gb|DV025685.1|DV025685

EST:     TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA                         GCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC
genomic: TTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAAC

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), 43 (downstream exon)
Score: 12

GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCAgtaagtagcc ... gttcttgcagGCACGATCTGGAGGTGAATGGTGGGAGGGGCCTAATTGTAGACCCAAGAACAAAGCACATATACCAGAGGACGTCCAGTTGATATATGCCAGTTCTGAGG

Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 22

Block sizes: 47 (upstream exon), 25 (downstream exon)
Score: 4