ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaacctttaacattttcttacaacttttacgctatttacttggatatatattaatactcatgttcattttaacaattttcag

Basic information

species	Zea mays
transcript	GRMZM2G174107_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 5'ss of exon 2

TATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgta-acctttaacattttcttacaacttttacgctatttacttggatatatattaata--------ctcatgttcat-tttaacaattttcag
 |||||||| |||  ||||||||||||||| || ||||| |  ||| ||||||||||||||||||||||  ||| ||| |||||||||||||| ||||||||| | |||| | ||| | | |||   ||| |  | ||||  ||| | | |||||| |        ||  || || | | |     |||||||
AATAAACATTACAACAGTTCAATTTGCTGTTGGTACTGTCGTTGCTTTGTTCATGTGGATCACTGGTATCCTTAGGAGACCAAAGATTTCTGGTGCACAGgtagatctttgatattgtttgacacacttt-cattgtttaaatgggt-tgtattaacaaggagtatctgttgctcttgtgttttccttttcag

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|93017132|gb|EB642652.1|EB642652

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGG
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGG

EST: gi|13198536|gb|BG354370.1|BG354370

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|148965579|gb|EE016409.2|EE016409

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|32850209|gb|CD989890.1|CD989890

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|149072176|gb|EE160417.2|EE160417

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|32841139|gb|CD980820.1|CD980820

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|32840783|gb|CD980464.1|CD980464

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|211399728|gb|FL235706.1|FL235706

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|32850098|gb|CD989779.1|CD989779

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|78180316|gb|DV550689.1|DV550689

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|148964314|gb|EC905711.2|EC905711

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|149078331|gb|EE167099.2|EE167099

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|149098082|gb|EE184035.2|EE184035

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|13558927|gb|BG550282.1|BG550282

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|148950588|gb|EC896170.2|EC896170

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|149082156|gb|EE171337.2|EE171337

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|211399721|gb|FL235699.1|FL235699

EST:     GTGGATTCACTGGTATTATTAAGAAGGCCAAAGATTTCCTGGAGCACCAG                         CTTGTAGCCAATCCTACC
genomic: GTGGAT-CACTGGTATTATTAAGA-GGCCAAAGATTTC-TGGAGCAC-AGgtaaccttta ... caattttcagCTTGTAGCCA-TCCTACC

EST: gi|211399724|gb|FL235702.1|FL235702

EST:     TCATGTGGATCACTGGTATAATTAAGAGGCCAAGGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACTTCTGGTTATTGTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTC

EST: gi|148937401|gb|EC881581.2|EC881581

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|24934366|gb|CA452584.1|CA452584

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

EST: gi|13150722|gb|BG321044.1|BG321044

EST:     TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAG                         CTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC
genomic: TCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTC

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), 48 (downstream exon)
Score: 35

TATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaaccttta ... caattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTCACCAACATGAGCCTTGGGAAAGTTGCAGTGTCATTTACGCACACCATCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 820

Block sizes: 38 (upstream exon), 39 (downstream exon)
Score: 7

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGAGGCCAAAGATTTCTGGAGCACAGgtaacctttaacattttcttacaacttttacgctatttacttggatatatattaatactcatgttcattttaacaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA