ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacctccgtttcaacggaacattcactctgaatgttccaatctcttgatattgagaaggtttccctctgttttttttcacag

Basic information

species	Zea mays
transcript	GRMZM2G144782_T03
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G144782_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g31850.2 (Oryza sativa), 5'ss of exon 8

GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacctccgtttcaacggaacattcactctgaatgttccaatctcttgatattgagaaggtttccctctgttttttttcacag-----------------------------------------------
||||||||||||| |||||||||| |||||| || ||||| || ||| ||||||||||||||||||| || |||||||| ||||||||   |||   |||| ||  |   | || |  | ||     ||  |   || |   | |     | | ||  ||| ||| ||                                                  
GGTGTTGCTACAGTAATGTCTTGAGGGATTCTCATCACTGTGTAGAAGGAGCAATGCATCACAACTGTCCTGTCTGCTTCGAGgtgag---ccttgctttccacaaa---tgcatttggtattcagaaaggtagagaaaaaaaaacaacattc-tcaatttgtttccagttcttgagatctgacataaaaaaatttgctctccttttccaaatcacag

upper sequence: GRMZM2G144782_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g31850.5 (Oryza sativa), 5'ss of exon 7

-----------------GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacctccgtttcaacggaacattcactctgaatgttccaatctcttgatattgagaaggtttccctctgttttttttcacag-----------------------------------------------
                 ||||||||||||| |||||||||| |||||| || ||||| || ||| ||||||||||||||||||| || |||||||| ||||||||   |||   |||| ||  |   | || |  | ||     ||  |   || |   | |     | | ||  ||| ||| ||                                                  
TATTCCTCACTAAACAGGGTGTTGCTACAGTAATGTCTTGAGGGATTCTCATCACTGTGTAGAAGGAGCAATGCATCACAACTGTCCTGTCTGCTTCGAGgtgag---ccttgctttccacaaa---tgcatttggtattcagaaaggtagagaaaaaaaaacaacattc-tcaatttgtttccagttcttgagatctgacataaaaaaatttgctctccttttccaaatcacag

upper sequence: GRMZM2G144782_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA11G19860.1 (Glycine max), 5'ss of exon 8

GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgaga--gacctccgtttcaacggaacattcactctgaatgttccaatct-cttgat----attgagaaggtttccctctgttttttttcacag
| |||||||||   || ||  || |  |    ||||  || || ||| |||||||||||||||| ||||| || ||||||||||| | |   |||||   | | | |  | | | |   |    |    |||||  |||||    ||| |||   ||||  | | |||    |  |||
GATGTTGCTACTCAAAGGTAATGGAAAAGGGGCACCGTTGTGTAGAAGGAGCAATGCATCACAATTGCCCTGTTTGCTTTGAGgtaaaacaaacctctagtactatgacagactgaaattttgggaagaaatctgtttgattctcatttagattatttcatttt-tttccccttgcag

upper sequence: GRMZM2G144782_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0007g04790.t01 (Vitis vinifera), 5'ss of exon 12

GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgaga-----gacctccgtttcaacggaacattcactctgaatgttccaatctcttgatattgagaaggtttccctctgttttttttcacag----------
| ||||||||    |  |  ||||||||||| ||| | || || |||||||||||||| ||||| ||||| || ||||| ||||| |       |   |  ||||    ||    ||   |   ||   |    | ||     ||| ||   ||||   | | |  ||||||| |           
GATGTTGCTATTCAACAGCTTTGAAGGATTCACACAATTGTGTGGAAAGAGCAATGCACCACAATTGCCCTGTTTGCTTCGAGgtaaactaattggtgtttgtttttttggc-tttttgttgaaaacaatttgttttc--agaatttaggttgtttgtttttttactttttcataacttattataa

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|71424311|gb|DR806292.1|DR806292

EST:     ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|74232676|gb|DT640590.1|DT640590

EST:     ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|71442410|gb|DR823460.1|DR823460

EST:     ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|18649707|gb|BM498526.1|BM498526

EST:     ACCACTGCGTGGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTCGAG                         TATCTGTTCGACTCCACAAAGGACATCAGTGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|61236803|gb|DN586530.1|DN586530

EST:     ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTCGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|71432840|gb|DR813890.1|DR813890

EST:     CCCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|78107357|gb|DV525775.1|DV525775

EST:     CTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: CTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|78089406|gb|DV517780.1|DV517780

EST:     CCCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: ACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

EST: gi|60396845|gb|DN229667.1|DN229667

EST:     AATGCATCACAACTGCCCCGTCTGCTTTGAG                         TATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC
genomic: AATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACC

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: 45 (upstream exon), 48 (downstream exon)
Score: 61

GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacc ... tttttcacagTATCTGTTCGACTCCACGAAGGACATCAGCGTGCTGCAATGTGGGCATACCATCCATTTGGAGTGCATGAACGAGATGAGAGCACACCATCA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 329

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 778

Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 29

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGCTACAGCAATGTCTTGAAGGATTCCCACCACTGCGTCGAAAGAGCAATGCATCACAACTGCCCCGTCTGCTTTGAGgtgagagacctccgtttcaacggaacattcactctgaatgttccaatctcttgatattgagaaggtttccctctgttttttttcacag

- - - - - - - - - - - - - - - - - - - - - - -  AGAGCA