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

...agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

Basic information

species	Zea mays
transcript	GRMZM2G032505_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 5

----agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttctt----gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
    |   |  || || || |   || | | |||   | |  | ||  ||||   |         ||||| ||    | | |||  || || ||    ||| |  ||||||||||| ||||||||||||||||| || |||||||| || |||||||| || ||||||||||| || || || || ||||||||||| ||||||||||
acatatgaacagccttgccttcagaagtctattta--tttactatttacttgcatatg------gttttctagcgcaacaataatcatatttttttgggcttgcccagATGTTTATCGGTGATGGAGCAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTG

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3

agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttca-------gATGTTTATTGGTGATGG----AGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
    ||     |      |  ||||  |||| || |||| || | ||||  | |||   |   |  | |     |||| |   |  | ||     ||||       ||| |  ||  |   |||    |||||| |||||||| ||||| || ||||| || ||||||||  |||| || ||||||||||| ||||| || |||||     
----atcaatctttttcagctaata-attttcttgtgat-ttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5

agacattgcattaccatggaaaatatgttttattctgatgt---tatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
      |  | ||   |   |  |  |||  ||  |    |   | |||        | | |   |||  | |     | |||            |  | ||||||||||| || || |||||||| ||||||| |||||| || ||||| || ||||||||  |||| || ||||||||||| ||||| || ||||| ||||
---atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5

agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctg--gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
     |   |  || |  | |||  |   | ||| |||| || |       | | ||| |     |||    || ||||||  | ||    ||   ||  ||||||| || || ||||||||||| |||||||| ||||| |||| |||||| ||||||||| | |||||||||||||| || |||||||| || || || |
----gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaac-caaacg-gaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5

--------------------------------------------------------------agacattgcattaccatggaaaatatgttttattctgatgttatct-tgagcacacttta-----tattttcaagtatgatagtaacgatgttcttgctggttca-----------gATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
                                                              |  | || |  |  | |||| |  |  ||||| | |  ||  | |  | |  |||  | |     |||  | |    |||| |||| ||  |  |  |   | ||           |||||| ||||| || ||||||||||||||||| ||||| || || |||||||||||||||||||| || ||||| || || ||||| || ||||||||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtc-tggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6

agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagt-atgatagtaacgatgttcttgctg---gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
    ||||  |     || ||||  |||     ||       ||  | |  |      || | | ||  | |  | | |||  || | ||||       | |||||||| || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||| | || ||||| || || |||||||| || ||||||||||
----attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5

-----------------------------------------------------agacattgcattaccatggaaaatatgttttattct-gatgttatcttgagcacactttatattttcaagtatgatagt-aacgatgttc-ttg-------------ctggttc--------agATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG
                                                      ||  |||  || || |      | |||  | | ||  || ||  | || |   | |     | ||||  |||  | || || | | ||| |||             ||| | |        ||||||||||||| ||||| ||||| |||||  |||| || |||||||| || || || |||||||| ||||| || || ||||||||  ||||||| ||||
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG

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|15589970|gb|BI674586.1|BI674586

EST:     CACAGACGAATGCCACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|149101526|gb|EE187649.2|EE187649

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|32932292|gb|CF037104.1|CF037104

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|60349052|gb|DN216025.1|DN216025

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|40303137|gb|CK347524.1|CK347524

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|60399057|gb|DN231873.1|DN231873

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|149077126|gb|EE165786.2|EE165786

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|32931353|gb|CF036165.1|CF036165

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|60341549|gb|DN208522.1|DN208522

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|149027737|gb|EE154581.2|EE154581

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|60398226|gb|DN231042.1|DN231042

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|148979720|gb|EE026793.2|EE026793

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|211370090|gb|FL332304.1|FL332304

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|60340215|gb|DN207188.1|DN207188

EST:     AATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: AATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|211024727|gb|FL157445.1|FL157445

EST:     CCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|74241693|gb|DT649607.1|DT649607

EST:     TTAGCTGGTCCACAAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: TTAGCTGGTCCAC-AACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|211467054|gb|FL315144.1|FL315144

EST:     TTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: TTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|67010865|gb|CO439614.1|CO439614

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|31558076|gb|CD527288.1|CD527288

EST:     AGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: AGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|149027738|gb|EE286068.2|EE286068

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCT
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGC-

EST: gi|149085415|gb|EE174921.2|EE174921

EST:     CGTTTTTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|211287069|gb|FL337511.1|FL337511

EST:     CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: CACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

EST: gi|149100562|gb|EE186647.2|EE186647

EST:     AATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAG                         ATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC
genomic: AATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCC

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), 47 (downstream exon)
Score: 348

GTACGGACCACCAGGAACTGGCAAGACACTCATGGCTCGTGCATGTGCTGCACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtt ... gctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 329

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 237

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

                             tagtaac  putative branch site (score: 237)
                                        ttcttgct  putative PPT
          tttatattttcaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -ttgcatt
- - - - - - - catggaa
- - - - - - - - - - - - - - - - -tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - -gcacact