ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...agcttttagctcatagttcagaagatgggcttgcaccagtctctgaagccattgatttctatattgctatgtcagtggcttattactatccatcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA

Basic information

species	Zea mays
transcript	GRMZM2G151529_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G151529_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g01290.1 (Oryza sativa), 3'ss of exon 2

agctttta----gctcatagttcagaagatgggcttgcacc---agtctctgaagccattgatttctatattgctatgtcagtggcttattactatccatcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA
||  || |    || || | ||         |  |||  |       |  ||||   | || | |||    |  | | |  ||  |||   || |   |    || |||   |||||||   ||||||||||||||||||| |||||  ||||||||| |||||||||| | |||||||| || ||||| ||||||||  |      
agtcttgagcaagcacacatttttttcccgtgatttgagcttaagacccgtgaatgtaatgttgtcttcccttgtttttttgttccttgaaac-acaaaagGCTCGGATGATAAGCCTGAGGCTGCACCTTACACCAGCGAAGAACTCATGAAAGTAATTGAAGAACAACTAGCTGCATCTGCAGCTGCTGCTTGGAATAC------

upper sequence: GRMZM2G151529_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g37130.1 (Oryza sativa), 3'ss of exon 4

agcttttagctcatagttcagaagatgggcttgcaccagtctctgaagc------cattgatttctatattgctatgtcagtggcttattactatccatca--ttcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA
   |  ||||    ||   || | |     ||   || ||   | ||||      |  ||| |   ||  |  | | |   | | |  ||   |  ||  |   || |||   |||||||   |||||||||||||||| || |||||  | |||||||||||||||||| | ||||| || || ||||| ||||||||  |      
-tttcctagccttgagca-agcacacatttttttccctgtgatttaagcttaagaccgtgaatgtaattctcttgttttttttgttccttgaaacacaaaagGCTCGGATGATAAGCCTGAGGCTGCACCTTACACCAGTGAAGAACTCATCAAAGTAACTGAAGAACAACTAGCTGCGTCTGCAGCTGCTGCTTGGAATAC------

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|211248880|gb|FL353272.1|FL353272

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATTCAAGCCTGC
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATAT-CAAGCCTGC

EST: gi|67010971|gb|CO439720.1|CO439720

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACCCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|149077405|gb|EE166095.2|EE166095

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|211314764|gb|FL362709.1|FL362709

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|71433878|gb|DR814928.1|DR814928

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTACCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|89252968|gb|DY624754.1|DY624754

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAN                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|18177007|gb|BM378217.1|BM378217

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|93015586|gb|EB641106.1|EB641106

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|18177055|gb|BM378265.1|BM378265

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACTTCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|32839855|gb|CD979536.1|CD979536

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|32839856|gb|CD979537.1|CD979537

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|26557399|gb|CA829634.1|CA829634

EST:     CAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: CAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

EST: gi|94474440|gb|EB703398.1|EB703398

EST:     TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAA                         ATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA
genomic: TTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAA

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: 56

AGCACTCTTGAACGAGAAATCGGAATTGATGAGGTTTCCCAGTCGACGAATTATACACCCACGACCATGAATAACAACCAACAACCTGCTGCCGACTCAAgttagtagat ... catcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 109

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aagccattgatttctatattgctatgtcagtggcttattactatccatcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA

    cattgat  putative branch site (score: 106)
     attgatttctatatt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcttttagctcatagttcagaagatgggcttgcaccagtctctgaagccattgatttctatattgctatgtcagtggcttattactatccatcattcagATATCAAGCCTGCACCTGCACCTTACACCAGCGATGAACTTGTGAAAGTAACTGAAGAACAAATTGCTGCATCAGCTGCTGCAGCTTGGAACCCGCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatg