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

...tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG

Basic information

species	Zea mays
transcript	AC235535.1_FGT001
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4

tctcatggaaaccaatcaataaggttttagttttcttgggccttgt-attctttgttcattgctttatg-taaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
|    ||  |   ||   |    ||   ||  |  |     ||  | | | | |||| | | ||  ||| | | | | |  |   || || |  |||  ||||||| || ||||||||| | ||||| ||| ||||||||||||||||||| ||||| |||||||||||||| |||||||| ||||| ||||||||||||
ttctttgtgattaaaatgagtccgtcacagactcgtgcaatctcatcagtttatgttaactactaaatgatcattatattcttgttggttta--cttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 4

---------------------tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttat-gtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
                       |  | | |||      |||||  | | | |  |      ||  || | |  ||| | |  |  || || ||  | || || || |||    || |||||| || ||||| |||||||| || || ||| ||||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||| |||||||| |||
gtgagctcctttcccttcacaattatttgtaactgtatcataagagtat-gctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatatattttttg--ctctgcagGTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 4

tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
| |  ||   | |||  |    | | |     ||  | |   || |  | ||| ||  |||  |  || |   |  |      | ||| | || || |||| ||| | || || ||| | ||||| ||  | |||||||| || ||||| |||||||||||||||||||| || ||||| ||  | |||||||| |||
tgtattgtctaacaaatacgtggatctattcatttatagtatttttgatttttttttcttgtgtcttgaatgctcattgcttgttttttattcattacagGTATCCAAGGGAAAATGAGGGATTACCAGCTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4

-tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
 | |  |  ||   |      ||    ||  |||         ||| ||| ||||||||  |  | ||| |   |  |  | | | ||| | ||||| |||| ||| | || || ||| | ||||| ||| | |||||||| || ||||| |||||||||||||||||||| || ||||| ||  | |||||||| |||
gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcac-gtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4

------tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
      |    |||  |  | |     |  || | | ||  |||    | ||||    ||||  |||     || || ||   |||   |||| |    |   |||||||| | || |||||| | ||||| ||| | ||||| || || ||||| |||||||||||||||||||| || ||||| ||  | || ||||| |||
tttttttactttggggattatttgtctaacttgtggattctttgtat-tcgtatctaatgttt-ttgtcacttg-aatttgacattgcttgttcg---ttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4

--tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
       | |       | || | |  ||    ||| |      | ||  |  |||||   |||  |                     ||   | |   |||| ||  ||||||||||| | ||||| ||| | ||||| || || ||||| |||||  ||||||||||||| |||||||| ||  | || ||||| |||
ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgtt--gtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG

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|149075149|gb|EE163643.2|EE163643

EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGT
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGT

EST: gi|22491353|gb|BU051276.1|BU051276

EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

EST: gi|19351041|gb|BM895573.1|BM895573

EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

EST: gi|20300252|gb|BQ163195.1|BQ163195

EST:     CCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: CCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

EST: gi|19350725|gb|BM895257.1|BM895257

EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

EST: gi|20300542|gb|BQ163485.1|BQ163485

EST:     AGATGCCC-TGCTGG-GCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

EST: gi|87153564|gb|DY398353.1|DY398353

EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

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), 48 (downstream exon)
Score: 479

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 214

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 178

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 282

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG

                                              tctttgc  CT-rich tract
                 tttatgtaaattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- -catggaa
- - - - - -ccaatca
- - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtttg