ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag

Basic information

species	Zea mays
transcript	GRMZM2G026470_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 5

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag
|| || ||||||||||| || || ||||||||||| | |||  |  |||||||||| || ||||| ||||| ||||| ||||| |||||||| |||||||||||||   ||||  |||    ||||        |||| | |  |    ||| ||| |      |  ||||| |   ||    | |     ||| | |  |   | |                                  
ATAGCTGTCTGCGCCGATGATCCTGAGTACCGCCATTTCAATAATCTCAGCGAGCTTTCTCCTCATCGCCTTCAGGAAATCCGGCGCTTCTTTGAAGACTgtacgc--ctgcttcctcagctcatacg----attgctacattttttatgcttggtatt-----gcaccttgatt--tcaattgttttattcttgatcaaaatctttcag-------------------------------

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|32831350|gb|CD971028.1|CD971028

EST:     TGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT

EST: gi|33098670|gb|CF058630.1|CF058630

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT

EST: gi|71331881|gb|DR802819.1|DR802819

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTTCTGCCCCGCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCC-GCC

EST: gi|78023075|gb|DV491462.1|DV491462

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTGGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAATGACTTCTTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|28984521|gb|BQ539133.2|BQ539133

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|71331880|gb|DR802818.1|DR802818

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|62550248|gb|DN830668.1|DN830668

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|60400572|gb|DN233379.1|DN233379

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT

EST: gi|78121801|gb|DV540185.1|DV540185

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|5499294|gb|AI855161.1|AI855161

EST:     CGAGCTCTCCCCTCNCCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|60354156|gb|DN221129.1|DN221129

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG

EST: gi|60344571|gb|DN211544.1|DN211544

EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT

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: 34 (upstream exon), 48 (downstream exon)
Score: 11

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 421

Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 53

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA