ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT

Basic information

species	Zea mays
transcript	GRMZM2G076049_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatcactctctatag-ttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                        ||   | || |   |||||  ||| | ||  |  | ||   ||| | |||||||  |    |||||    |   |   | |   || | |||||   |||||||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||
-----------------------gtacgtattctcgtcctataacttggcgttaagaatgtac--tactggtgaagcagcat---tgtgatttgtga-gtaacctgctgtggccgcgtg-tagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                               | | | ||| |  |    | |     | |||| |      |||  | ||      | |        |   ||||  || ||    |  ||||||||  |||  |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| |  |||||||| || ||||||| |
------------------------------gtaagtttct-tgttctgttatgaaaatgtagattgatagagaa-tatgatgatgattaatgaggtaggcacattgtgttgtttact--cagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                           ||| |   ||| | | |||         |  | || |||      |   || |      | |        |   ||||  ||  |    |  ||||||||  ||| ||||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || ||||  |  |||||||| || ||||||| |
--------------------------gtaagtttttctgttttgtt---------ctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttct--cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatc-actctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                           ||| || |||||    |  | | |||    ||      |  | ||     ||    | | | |   || |  ||  ||||          |  ||||| ||  |  |||| || |||||||||||||| |||||| | |||||||| || ||||||||||||||  | ||| |  | || ||| |  | ||||| |
--------------------------gtaagtctactctactaacatacatttcaaact------tctccttcttctaa----tctctaacttttccgacgatatttcaaaa----atctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1

-------------------------gtacgtgcaccgacccagtccgactaataaatcac---tctctatagttgc---cttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgta-acagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                         |||   |||   ||      |  | | |  ||  |   |   | |   ||    |||||   |     | |         ||  || || ||| |   | |||  | |  | ||| | | | |   ||||| ||| |||  ||||||||||||||||| || |||||||| ||||||||| | || ||||| ||||  |   |  |  |||| |||||   | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgct-gaaat-tgtaaaattgaccttgacgat-ggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                                    |  || | |    |  | |  |  |  ||     |   |    || | | |         ||  | ||||  |||  ||    |||||| |||| || ||||| ||||||||  | ||||||||||| ||||| || ||||||||||||||||||   |||||  |||||||| || || | || |
---------------------------------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctag------tcgatcgattt--tcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
                                      | ||||   | |||   | | |  | |    ||   |      |  | |     |   ||  | ||||  |||  ||    |||||| |||| || ||||| ||||||||  ||||||||||||| ||||| || ||||||||||||||||||   |||||  |||||||| || || | || |
-----------------------------------gtaccatagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttc----tagtcgatcgattt--tcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

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|5268634|gb|AI770598.1|AI770598

EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

EST: gi|211132427|gb|FL330812.1|FL330812

EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGAG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

EST: gi|211531487|gb|FL328402.1|FL328402

EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

EST: gi|5268673|gb|AI770637.1|AI770637

EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

EST: gi|71762692|gb|DR960629.1|DR960629

EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

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 2 RNA-Seq libraries.

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80

CATCCTCTTCTTCGAGGGGCAGCGCTCGGGGAGGCTCCCGCCGGACCAGCGCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT