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

gtaagacaataacggctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT

Basic information

species	Zea mays
transcript	GRMZM2G171688_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 2

gtaagacaataacggctgaataaatttcagtatatttccactatgttcatccggctt-aagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT
         | | ||   |  | |  ||| ||| |||  |||   || || | |||| ||   ||| |||||||| ||||||  ||||||||||||||||||||||| || ||||| ||||| |||||||||||||||||||||||||| ||||| ||||| || || |||||||| || ||||||
--------gtga-ggtcaagaacagctcaatatttttgtacttcatttattctgctttaaacttatgtgcttcctcggtttt-tagGTATATGAGGCCAGAGACAGCACAAGGTATCTTTGTAAACTTCAAAGACTTGTATTACTACAACGGCAACAAGCTACCCTTTGCTGCAGCACAGATTGGT

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 2

gtaagacaataacggctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT
|||||    |||   ||        ||||||    ||| | |  ||  |  |     || |   | ||||    ||    |||||||||||| | || || |||||||| || |||||||| || || || |||||||| || || |||||||  ||||| || || |||||||| ||||| |||
gtaaggatttaatttctatt---gcttcagttgtattcaatttagtataggcatgccaatttcttttgctcatctga---tgcagGTATATGCGCCCTGAAACAGCTCAAGGAATATTTGTAAATTTTAAGGACTTGTACTATTATAATGGCAGCAAGCTTCCCTTTGCTGCAGCTCAAATCGGT

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2

---------------------------------------------------gtaagacaataacggctgaataaatttcagtatatttccact------atgttcat-------ccggcttaagtgtatctgcttccttggtt------------ttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT
                                                    || |  | | |      ||  |   || || ||||  ||||      || |||||       | | ||||  |    |||  |  ||  ||             || ||||||||| ||||||||||||| ||||| || ||||| |||||||| ||  |||||||||| ||||| || ||||| || || |||||||| |||||||||
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S310_3V6.1 (Physcomitrella patens), 3'ss of exon 1

gtaaga----caataacggctgaat------aaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT
||||||     ||    || |   |        | | || ||  |      |   | |   |    | |        |  || |  ||    ||| ||||||||||| |||||||| || || || |||||||||||||  || ||||| ||| | | ||| ||||||||||| |||||||||||||| ||||||
gtaagagtcctaaccttggtttcttccctttggagtccattacgtgaagcttgaatgctcgcaaactgaaacctgtggggtcttctgtccaacagTTATATGAGGCCGGAGACAGCACAAGGCATTTTTGTGAACTTCAGGGATTTGTACTACGAAAGTGGTAATAAGCTGCCTTTCGCTGCAGCCCAGATTGGT

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|211446350|gb|FL194324.1|FL194324

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCANAGACAGCTCAGGGTATATTTGTGAACTTC
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTC

EST: gi|148972573|gb|EE023537.2|EE023537

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446351|gb|FL194325.1|FL194325

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|13126604|gb|BG317174.1|BG317174

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|60342069|gb|DN209042.1|DN209042

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446352|gb|FL194326.1|FL194326

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|47961805|gb|CN844514.1|CN844514

EST:     TTAATCTCATGTTTCAAACTTCCATTGGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTAATCTCATGTTTCAAACTTCCATTGG-ACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|31354132|gb|CD438489.1|CD438489

EST:     TTTAATCTCATGTTTCAAACTTCCATCGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446355|gb|FL194329.1|FL194329

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446353|gb|FL194327.1|FL194327

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

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: 289

ATAAGATTGTTGCTCCAGACACCAAGAACTCATTATCAGATCCATACCCTTTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 160

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT

                                      cttccttg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacaataacggctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG