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

...tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA

Basic information

species	Zea mays
transcript	GRMZM2G024668_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1

tcatcccttgtttgtgctatactcttattactgcatggttaggctgcacta---ggttgtatgcatcaaaccaacg---aactgtttcttta---ttgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
         |   |||| | |   ||  |  |  |  |  |  | | | |    | |||||||  |  |          |  |||| |||||   |||   ||   ||||||||||| ||||| ||||| |||    | || |||||||||||| ||||||  ||||| ||||||||||| || || || || |||||||||||||| |
---------ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S83_80V6.1 (Physcomitrella patens), 3'ss of exon 1

---tcatcccttgtttgtgctatactct--tattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
     |    |  ||||   | | |  |  | |  || | || ||     |   | |  ||| ||   | | ||   ||||||| | | | || | |  |    |||| |||| |||||| | ||||||    |||| |||||||||||||| |||| |||||| ||||| |||||||| ||| | || |||||||| |||||||
tgtgtaggtttactttgaaatgtgccgtgatgtgtctacgtgtttgaaagggtgttgagtgt-tgttgccatcccctgaactgtatttgtcttatgttta----gGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGATGGCCAGCCAGAGCTCTTCATCCATATCATTCCCGACAAGGCGAACAATA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22362 (Selaginella moellendorffii), 3'ss of exon 1

----tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaa--ccaacgaactgtttctttattgtttccaaa--cagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
       |    || | || |     | || | |||||     |   |     | |  |   | |  | |   |  ||  |   || | || ||  | | |    |||||  | || |||||  |||||||  |  |||| |||||||||||||| ||   |||||||||||| |||||||||||||| || |||||||| | ||| |
gtgagtgttagatgctcgttcggcgatatt-tcactgcgattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcgttctttctgcgatttccagGCTCTCGACAAGATTCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 1

tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaac-agGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
                           | | |   | |    | |   | || |  | |  | |           ||  | ||    || |   |  | ||||  | || |||||| | |||||  |  | || |||||||| ||||| ||   |||||||||||| |||||||||||| |||| |||||||||| ||| |
--------------------------gtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccagGCTCTCGACAAGATCCGCTTCGAAGGCCTCACTGACAAGAGTAAGCTTGAGAGCCAGCCGGAGCTCTTCATCCACATCATCCCCGACAAGGCCAGCAAGA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 1

tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
        ||  | |        ||| ||  | || | |   |    |||    | | | | ||  |        |||   |  | |   | |     ||||  | || |||||| | |||||  |  | || |||||||| ||||| ||   |||||||||||| |||||||||||| |||| |||||||||| ||| |
-------gtgagtatttcgcctccttgttcttcca-gttcttgtcaaact---ctttcttcttctcat------gctgcgccgctgtgactcc-----agGCTCTCGACAAGATCCGCTTCGAAGGCCTCACTGACAAGAGTAAGCTTGAGAGCCAGCCGGAGCTCTTCATCCACATCATCCCCGACAAGGCCAGCAAGA

upper sequence: GRMZM2G024668_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25533 (Selaginella moellendorffii), 3'ss of exon 1

----tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaa-----cagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA
       |    || | || |     | || ||||||| |  |      |  ||  |   | |   |   |      | |  | | |  ||| ||||         |||||  | || |||||| |||||||  |  |||| |||||||||||||| ||   |||||||||||| |||||||||||||| || |||||||| | ||| |
gtgagtgttagatgctcgttcggcgatatt-ttactgc-tattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcattctttctgcgatttccagGCTCTCGACAAGATCCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA

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|20208311|gb|BQ134400.1|BQ134400

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAATATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|22521360|gb|BU080171.1|BU080171

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18649392|gb|BM498211.1|BM498211

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18450519|gb|BM428797.1|BM428797

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGGTCGAGAGTNTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18648849|gb|BM497668.1|BM497668

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18649320|gb|BM498139.1|BM498139

EST:     ACTCCAAC-AGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCC-TGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|19822707|gb|BQ048731.1|BQ048731

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|22818773|gb|BU498863.1|BU498863

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|211138726|gb|FL294024.1|FL294024

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|21843518|gb|BQ704099.1|BQ704099

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18648810|gb|BM497629.1|BM497629

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCTGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|20802426|gb|BQ293476.1|BQ293476

EST:     AGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: AGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|22542460|gb|BU092898.1|BU092898

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18649426|gb|BM498245.1|BM498245

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|16746046|gb|BM032476.1|BM032476

EST:     ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

EST: gi|18450520|gb|BM428798.1|BM428798

EST:     ACTCCAAC-AGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGAT                         GCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT
genomic: ACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGAT

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: 815

CTTCCAGGCGGAGATCAACCAGCTGCTATCGCTCATCATCAACACCTTCTACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagtttca ... ttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 372

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1127

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA

                                 tttctttattgtttcc  CT-rich tract
                                 tttctttattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatcccttgtttgtgctatactcttattactgcatggttaggctgcactaggttgtatgcatcaaaccaacgaactgtttctttattgtttccaaacagGCCTTGGATAAGATCAGGTTCGAGAGTTTGACGGACAAGAGCAAGCTGGATGCCCAGCCGGAGCTGTTCATCCACATCGTCCCTGACAAGGCCAACAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-catccct
- - - - tgtttgt
- - - - - - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - gctgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacgaa