ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagtttcattctggccatgtcgatcgatcgaattctcatgctgcggcgcgagttcatgactgaccttggatttgaactattattattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT

Basic information

species	Zea mays
transcript	GRMZM2G081843_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G081843_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57720.1 (Oryza sativa), 3'ss of exon 1

gtgagtttcattctggccatg--tcgatcgatcgaattctcatgctgcggcgcgagttca--tgactgaccttgg--atttgaactatt-attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT
   |  ||| || |      |  | ||  ||     | || ||  |    ||  | || |  | | |||     |  | ||||   ||  |||  |||||||||| ||||||||||| || |||||||| || || || || |||||||||||||||||  | ||||| ||  |||||||||||||||| |||| |||| 
acaaaattcgttttttatgggatttgagggagtagttgctaataatcacacgttaatttagttcattgattagtgctaattgatggatggatttgtgcagTGGATTTTCTGGGTTGGTCCGTTCATCGGAGCGGCACTGGCGGCCATCTACCACGTGGTGGTGATCAGAGCAATCCCCTTCAAGAGCCGGGACTAATTAA

upper sequence: GRMZM2G081843_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G42220.3 (Glycine max), 3'ss of exon 3

-------------------------------------gtgagtttcattctg-gccatgtcgatcga----tcgaattctcatgctg-cggcgcgagttcat--ga--ctgaccttggatttgaactattattattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCC-GTGACTGATTAT
                                      |   ||||||| |  || || |   || |    | || || ||  |    ||   |  || | |  ||  ||||   |   | |      || |   ||||||||||||||||||| || || ||||| |||||||| ||||| ||  ||||||||  |||| | ||||||||| | |||||||||  |  |||| | | |  
gtaagttgttaattgattcatttatttcataattgctatttttttcattttacgcaatatttgtccaattttagatttttcgggaaaacgaatctggtccgtctgattctgatgcttattgtttgtcgttttctgtgcagTGGATCTTCTGGGTGGGACCTTTCATTGGTGCTGCACTTGCAGCACTCTACCACCAGGTCGTAATCAGGGCCATTCCCTTCAAGTCCAAGTGATTCAATC-

upper sequence: GRMZM2G081843_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G06680.2 (Glycine max), 3'ss of exon 2

-----------------------------------------gtgagtttcattctggccatgtc-gatcgatcgaattctcatgctgcggcgcgagttcatgactgaccttggatttgaactattattattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCC-GTGACTGATTAT
                                            |   |||||    | || |  |||   |||      |    |  || |||  || ||  |||||  |   | |      || |   ||||||||||||||||||| || || ||||||||||| |||||||| ||  ||||||||  |||| | ||||||||| | |||||||||  |  |||| | | |  
gtaagttgttaattaattcatttatttcataattggtaaaaaaaaaaatcattgaaccaattttagatttttcgggaaaacgaa-tctggagcgt-ttgatctctgacgcttattgtttgtcgttttccgtgcagTGGATCTTCTGGGTGGGACCATTCATCGGTGCAGCTCTTGCAGCACTCTACCACCAGGTCGTAATCAGGGCCATTCCCTTCAAGTCCAAGTGATTCAATC-

upper sequence: GRMZM2G081843_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 3'ss of exon 3

gtgagtttcattctggccatgtcgatcgatcgaattctcatgctgcggc-gcgagttcatgactgaccttggatttgaactattattattgc----agTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT
|| || | |||  |  |     | |||  |     ||||||  |    | | || |   || ||    |||  ||    || || || || |    ||||||| ||||||||||| |||||||| || ||||||||||| ||| | ||||||  | |  | ||||| ||| |||| ||||||| | | | ||||  | 
gtaagctccatgat--cagacccaatcacttctcatctcatcatttatctgtgaatc--tgccttgtattgatttcattcttttgttgttcccttcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTACCACCAGATAGTAATCAGAGCCATCCCATTCAAGACCAGAGCCTGAGAAA

upper sequence: GRMZM2G081843_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 3'ss of exon 3

----------------------gtgagtttcattctggccatgtcgatcgatcgaattctcatgctgcggcgcgagttcatgactgaccttggatttgaactattattattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT
                         |     |     |  || | |     |   ||  | |   ||  |    |||||| |       |  || ||    | |  |  || ||||||||||||||||| || || ||||| || ||||||||||| ||||| |||||   | |  ||||||| ||| | || ||||||||| | |  |||   |
gtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaaattg-agtttcagttcaagttcttattgtgactttttttctcttgctttcagTGGATCTTCTGGGTGGGACCGTTCATTGGAGCTGCTCTTGCTGCCATGTACCAGCAGATAGTCATCAGAGCCATTCCATTCAAGAGCAGGGCTTGAGATT

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|76286572|gb|DV026140.1|DV026140

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTTTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|5740629|gb|AI948319.1|AI948319

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGAAAAA                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|71304469|gb|DR788350.1|DR788350

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|78022837|gb|DV491224.1|DV491224

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|5525247|gb|AI861086.1|AI861086

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|37400918|gb|CF637819.1|CF637819

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|8273153|gb|BE012244.1|BE012244

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGAGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

EST: gi|149027065|gb|EE046387.2|EE046387

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTA
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTT-CTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTA

EST: gi|44900250|gb|CK826795.1|CK826795

EST:     GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCAC                         TGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC
genomic: GCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTAC

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

GCACCTGGCGACCATCCCCATCACCGGCACCGGCATCAACCCCGCGCGCAGCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttca ... attattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 897

Block sizes: 39 (upstream exon), 31 (downstream exon)
Score: 10

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catgctgcggcgcgagttcatgactgaccttggatttgaactattattattgcagTGGATCTTCTGGGTTGGCCCCTTCATCGGTGCTGCTCTTGCCGCCATCTACCACGTGGTCATCATCAGGGCCCTCCCCTTCAAGAGCCGTGACTGATTAT