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

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

Basic information

species	Zea mays
transcript	GRMZM2G056393_T01
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 11

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
   ||||   ||||  ||    | |     | |||||||   | |||  |||| || ||||   || | |  |   |      | |||||||||||||| ||||||||||| ||||| || |||||||||||||||||||| ||| ||||| | || |||||  ||
--gtatctacttttctattttcaag-----aatgctatattaactttaataccatacatgtgacaaataattaattaaaataacatttcagTTTTCAAAGGCTCTGAATCGTTTCCAGAAAGAGGATCCTACTTTCCGTGTAGGTCTGGATCCAGAAAGTGGAGAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 6

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgtta--ccctagatgtcctaagtgaaaatacacct--atccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
||   | || | ||| ||  ||   || | ||  ||   |    ||||  |  |  |  ||  ||||| || |  |     |  ||  ||| ||||||||||||||| |||||||||||||||| || |||||||| || ||||| || |||||  | |||||||| |||
gtgagtaatttattttatgtaacatgt-caacccctgccctagatttgaaaaacgttgtatcacctaattggatttctctgtgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACATTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctag-atgtcctaagtgaaaatacaccta-tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
||   | || | ||| ||  ||   ||    |  ||    | | ||    |   | | ||  ||||| || |  |   |  | |  ||| ||||||||||||||| |||||||||||||||| || ||||||||||| ||||| || |||||  | |||||||| |||
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11

-----gtatatcatatttttcatcaaaagggtacgactgctatacat-agtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
      ||| | |  |||       |||    |  |    | | | | | | || |       |  |   || ||||| |  |  |  |  | | |||| || ||||| |||||||| ||||| || |||||||||||||||||||||||||||||| | ||||||||||||
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaa-tctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 11

-----gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
      | | | |  |||      ||||  | |  |    | | | |   || |     || |  |    |    ||||  |  | |   | | |||| || |||||  ||||||| ||||| || |||||||||||||||||||||||||||||| | ||||||||||||
gtaacttctgtgaactttgaagctaaaacagcaacatatttttccttcaattctggttttaaacatttgcaactgaaatctattttttggtgttagTTCTCGAAAGCATTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 11

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttacc--ctagatgtcctaagtgaaaata--cacctatcccttt-cagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
                 | |  | ||  | | ||  |||   | ||  ||     ||    || | || |||   ||      ||||| | | ||||||||||| ||| |||||||||| || |  |||||||||||||||||||| || ||||| ||||||||||| |||
----------------gtgagtacggc-caattgagatatcaatttactttgtaactgatggtaccaaatgatggtaattttttatccttgtacagTTTTCAAAGGCTTTGAATCGCTTTCAGAGAGAGGATCCTACTTTCCGTGTTGGGTTGGACGCTGAGAGTGGGCAG

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|32930091|gb|CF034903.1|CF034903

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAA                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|91874831|gb|EB404788.1|EB404788

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|6194594|gb|AW146698.1|AW146698

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|211410070|gb|FL355701.1|FL355701

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|118406757|gb|EH038205.1|EH038205

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|211409847|gb|FL347405.1|FL347405

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|67017174|gb|CO445923.1|CO445923

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

EST: gi|211430479|gb|FL350077.1|FL350077

EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 206

TACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 183

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

                                       cacctatccctttc  CT-rich tract
                               tgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG