ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGGAGCCGAAGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgctaatgacaccaatcgaccaatccatcatgtgcattccattagttttaattaagggttgggaaacatcacctagaaatcccaaaacttttga...

Basic information

species	Zea mays
transcript	GRMZM2G107896_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107896_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g39720.4 (Oryza sativa), 5'ss of exon 4

GTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGGAGCCGAAGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaattt---gctaatgacaccaatcgaccaatccat-catgtgcattccattagttttaattaagggttgggaaacatcacctagaaatcccaaaacttttga
| ||  |  |  | |||||||| || |  ||     |   |||  | || ||||||||||| ||||||||| | || ||||||||||||||||| |||||||||| |   | || || |  ||| |   |  |  |   ||| | | |     | |  ||  |  |  |    | |      || |    ||    |  |    
GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgtaaagttattgtcttcaaacaggctctgtagatatgagtaatgacaaaatgatatcttggcatccctagattctttcttgttggccagccaaat----

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|22521256|gb|BU080067.1|BU080067

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAG
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAG

EST: gi|71758024|gb|DR955961.1|DR955961

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|101385910|gb|EB815003.1|EB815003

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCC

EST: gi|61236552|gb|DN586301.1|DN586301

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|71436668|gb|DR817718.1|DR817718

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAATTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|76287872|gb|DV027440.1|DV027440

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|78117243|gb|DV535630.1|DV535630

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|20803428|gb|BQ294478.1|BQ294478

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGT
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGT

EST: gi|91878775|gb|EB408732.1|EB408732

EST:     AGTCGCCCCCGGAGCCCAAGACATCGAAGGAGCCCCAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGG
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGG

EST: gi|211100312|gb|FL296769.1|FL296769

EST:     CAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATNGCANAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACANCAGGTC
genomic: CAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|71430644|gb|DR811694.1|DR811694

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|89756366|gb|DY686416.1|DY686416

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|32908752|gb|CF013565.1|CF013565

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|71429329|gb|DR810379.1|DR810379

EST:     GTCGCAGCCGGAGCCCAAAGACATCGAAGGACCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAG
genomic: GTCGCAGCCGGAGCCCAA-GACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAG

EST: gi|76014171|gb|DT941341.1|DT941341

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|50326567|gb|CO521693.1|CO521693

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|78081066|gb|DV509478.1|DV509478

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|76014170|gb|DT941340.1|DT941340

EST:     AGTTGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|71595874|gb|DR906625.1|DR906625

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

EST: gi|78113845|gb|DV532234.1|DV532234

EST:     AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAG                         GAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC
genomic: AGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTC

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: 97

GTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGGAGCCGAAGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgct ... gggttttcagGAGCTACAGCCCACGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCGCCACTGCCACCACCGCCTCCTAGAAATAACAGCATGTCACCACGG

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 65

Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 54

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGGAGCCGAAGTCGCAGCCGGAGCCCAAGACATCGAAGGAGCCCAAGCTATGGCAGAAGgtaatttgctaatgacaccaatcgaccaatccatcatgtgcattccattagttttaattaagggttgggaaacatcacctagaaatcccaaaacttttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT