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

...ctttaatgctctatgacgcacatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttgtacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC

Basic information

species	Zea mays
transcript	GRMZM2G040369_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G040369_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g02820.1 (Oryza sativa), 3'ss of exon 2

----cttta-atgctctatgacgcacatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttgtacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC
    || |  | ||  |   || |   |||  || |||||| |||   |  |     || ||| || |  ||    ||    |   | ||||   ||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||
ttggctatgcaagcatttcaactcttctgt-aaatttgctgctgaccattcca----ttttctgttagaaatacactatgctaatatgttatgtgttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACCCGTGCAGATGAAGC

upper sequence: GRMZM2G040369_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32030.1 (Oryza sativa), 3'ss of exon 2

ctttaatgctctatgacgc--acatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttgtacctg-atgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC
| |  ||  |  ||| |       |||  || ||    |   | |   |     || | |     |||   || || |  |||||||  |    ||| |||||| |||||||| ||||| ||||| |||||||| |||||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||
catctattttagatggctttgttttgtgcaaattttcagctttctatgccttagttttgtgcaaatcaaggtgcacttacatgctatgttc---tctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCCAGGAAGTTGCGGGTGATGTTCGCATGACTGATACCCGTGCAGATGAAGC

upper sequence: GRMZM2G040369_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 2

-ctttaatgctctatgacgcacatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttg-tacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC
  | || |   || |      | | ||    |||||| |         |  | |    ||  ||  |   || |   |||| || |||| | ||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||| |||  ||||||||||
aatatattatgctcttgttttcctatttgt-ttgctgattcaacatcttgagttatatttgatgcaacaatgatgtttgat-ctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC

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|211405049|gb|FL246108.1|FL246108

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGACC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|33092863|gb|CF052857.1|CF052857

EST:     ATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATCCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: ATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211399956|gb|FL246074.1|FL246074

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211402514|gb|FL246099.1|FL246099

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|9732387|gb|BE511139.1|BE511139

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211316749|gb|FL246047.1|FL246047

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|5555619|gb|AI881570.1|AI881570

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211316754|gb|FL246052.1|FL246052

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211402513|gb|FL246098.1|FL246098

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|148979512|gb|EE026695.2|EE026695

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|31355298|gb|CD439655.1|CD439655

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211407593|gb|FL246116.1|FL246116

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211314734|gb|FL246039.1|FL246039

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|31353201|gb|CD437558.1|CD437558

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|18384461|gb|BM417660.1|BM417660

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|211402512|gb|FL246097.1|FL246097

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|20300440|gb|BQ163383.1|BQ163383

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|31361705|gb|CD446062.1|CD446062

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|19770476|gb|BQ035197.1|BQ035197

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|32945682|gb|CF050501.1|CF050501

EST:     ATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAGATCCCCTTGTGGCAGCTGCTGGTATTATTGCCC
genomic: ATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

EST: gi|29167841|gb|CB411101.1|CB411101

EST:     CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATG                         GCAAGTCTACGCTTACAAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCC
genomic: CAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTAC-AGATTCCCTTGTGGCAGCTGCTGGGATTATTGCC

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: 1835

GAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcag ... ttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1332

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 625

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 918

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctaggcttatctttttgtcatcttgtacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC

                           acctgat  putative branch site (score: 918)
                                         ttacttcttt  putative PPT
                                    tattattacttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaatgctctatgacgcacatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttgtacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - aatgctc
- - - - - - - gacgcac
- - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc