ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattactagggtgcaaatggttggat...

Basic information

species	Zea mays
transcript	GRMZM2G049672_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g55200.1 (Oryza sativa), 5'ss of exon 4

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatg-attactagggtgcaaatggttggat
|||||||||| ||||||||||| ||||| ||||||  |||||| |||  ||| || ||||| || |||||||||||||||||||||||||||||||||||||| | |  ||  |||||    | ||     | ||||     | |  || ||  |   | |    |    ||  |  |    |   |  | | | |||  |
TGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAACTGTGTTCTCAACTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtacggcaattttctcttggggacttgagg-atatgtgaacctgctattgatacgtttattgcctactccctccgtgtctaaataattgacacgtttgact

upper sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g01420.2 (Oryza sativa), 5'ss of exon 3

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattacta--gggtgcaaatggtt-ggat
|||||||| | ||||||||||| || || ||||||  | |||| |||  ||| || ||||| || |||||||||||||||||||||||||||||||||||||| | |  ||  |||||    | |        || | | |   |     ||    |   | | |   ||||   | | |    | ||  ||||  ||   ||
TGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACAACCAAGAACTGTGTTCTCAACTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtacgacaattttctcttggggactgga---ggatatatgtgaacctgctattgatacgtttatagcctactcctactccctccgtgtctaaataatttacat

upper sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G47010.1 (Glycine max), 5'ss of exon 4

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattactagggtgcaaatggttggat--
| |||||||| |||||  | ||  ||||| ||      |   | |  | |||  ||||||||||||| ||||| || || || |||||||| |||||||||||||| |  | |||||   ||| | ||| | |        ||  |||   | | ||  ||   |   |  | |   |  ||| |   | ||   |   |  
TCTGTGCAGAGGACATTCGTGATCAGTTAGAAAAAGTTGGTAACACTTCAGAGTTATGTTCACAGCTAGGAGCAGTCTTGGGTATGCTTGGTGACTGCTGgtatgttttcttgctctcttctactccccaccacc--cgcgatctactgactaatcagtctgttactcttattttcctgttagtgcatatatctatctttca

upper sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G15130.1 (Glycine max), 5'ss of exon 4

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatacta-tgattactagggtgcaaatggttggat
| |||||||| |||||  | ||  ||||| ||      |   | |  | |||  ||||||||||||| ||||| || || || |||||||| |||||||||||||| |  | |||||   |||   |||     ||   | |     || |||||     |      ||  |  || ||       |   |||  ||    
TCTGTGCAGAAGACATTCGTGATCAGTTAGAAAAAGTTGGTAACACTTCAGAGTTATGTTCACAGCTAGGAGCAGTCTTGGGTATGCTTGGTGACTGCTGgtatgttttcttgctctcttctaccccccctccctgcagtcaactggttaatcagtctgttgctcttattttcctgtttgtgcatatatcaatctttcat-

upper sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctctt--aactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattactagggtgcaaatggttggat
| || ||||| || ||| | |   ||||  ||      |   | |  |  ||  | |||||||| || ||||| ||  |||| ||||||||||||||||||||||||  ||  || ||    ||  || | |    |     |||  | ||   |       |      | |  |||  |    || |  |  |||      
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataattatcctttggtgtgcatttagagcatgtctttgtggttttagttggcact--

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|60340202|gb|DN207175.1|DN207175

EST:     GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTG                         TCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC
genomic: GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

EST: gi|67021056|gb|CO449805.1|CO449805

EST:     GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTG                         TCGGACCTTGGGAGATGTTCCTGCAGCAATCACTTACTATGAAGAAAGTGC
genomic: GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

EST: gi|33094944|gb|CF054938.1|CF054938

EST:     GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCCTGGGGACTGCTG                         TCGGACCTTGGGAGGTGTTCCTGCAGCAATCACTTACTATGAAGAAAGTGC
genomic: GACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

EST: gi|32909333|gb|CF014145.1|CF014145

EST:     TGCTTGGGGACTGCTG                         TCGGACCTTGGGAGATGTTCCTGCAGCAATCACTTACTATGAAGAAAGTGC
genomic: TGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

EST: gi|32909332|gb|CF014144.1|CF014144

EST:     GCTTGGGGACTGCTG                         TCGGACCTTGGGAGATGTTCCTGCAGCAATCACTTACTATGAAGAAAGTGC
genomic: GCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

EST: gi|16925308|gb|BM078376.1|BM078376

EST:     TGTTAGGAATGCTTGGGGACTGCTG                         TCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC
genomic: TGTTAGGAATGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGC

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: 161

TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgt ... gtgttttcagTCGGACCTTGGGAGATGTTCCTGCAGCAATCACCTACTATGAAGAAAGTGCTGAGTTCCTCTCAAAGCCCCCTGCAAAAGATCTTGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctcttaactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattactagggtgcaaatggttggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaat