ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacag

Basic information

species	Zea mays
transcript	GRMZM2G073498_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 4

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattt-tattgctatcacag
 || || ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  | || ||| ||||| |||| ||| |||  |  ||||   ||| | ||| ||     | |  | ||| ||||||| |  |||
CGGTCAACAAGGCTCATACCCAATTAAGCTGTTCTACACTTCAAACATGCCCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttag-cattaacatgtttgtattgctttggcag

upper sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 1

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacctcatttccaatgctgta---gtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacag
||| ||||| || |||||||| || ||||| |||||||| || ||||||||||||||||| || ||||| ||  |||||||||| || || |||||||||||||       |  |  ||   ||||     | ||   |     | | |    |||| | | || |   |||||||| |  | ||||
TGGACAGCAGGGTTCATATCCTATCAAGCTGTTCTACACCTCCAACATGCCCATCATTCTACAGTCTGCTCTTGTTACCAACCTATACTTTATATCCCAGgtac----tggagctttaagcttgtatacacaggttggggtcattttcttctggtgtta-tactaaca-attttatttc--ttacag

upper sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0076g00240.t01 (Vitis vinifera), 5'ss of exon 1

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacctcatttccaatgctgta---gtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacag
||| || ||||| |||||||| |||||| | |||||||| || ||||||||||||||||| || | ||| ||  || ||||| | || || |||||| ||||||     | |  |  ||   ||||    | | |         | | |    |||| | | || |   |||||||| |  | | ||
TGGACAACAAGGTTCATATCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTACAATTTGCTCTTGTTTCCAACATTTACTTTATATCCTAGgtac----ttgagctttaagcttgtatacatgaattgcagtcattttcttctggtgtta-tactaaca-attttatttc--ttatag

upper sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 5'ss of exon 4

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacctcatttccaatgctgta---gtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacag
||| ||||| || |||||||| |||||||| |||||||| || ||||||||||||||| | || ||||| ||  || ||||||| || || |||||||||||||     | |  |  ||   ||||    | |||   |     | | |    |||| | | || |   |||||||| |  | ||||
TGGACAGCAGGGTTCATATCCTATTAAGCTGTTCTACACCTCCAACATGCCCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtac----ttgagctttaagcttgtatacatgagttgcggtcattttcttctggtgtta-tactaaca-attttatttc--ttacag

upper sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 5'ss of exon 4

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtac---------gcacctcatttccaatgc-tgtagtaagtcatgtcttctgtg-tgt-atgtgtaaatgctgatgtatt----ttattgctatcacag-------------------------------------
||| || ||||| || ||||| || || ||||||||||| || ||||||||||||||||| ||   ||| ||  |  ||||| | || ||||| || ||||||          |   ||  | | ||||   |  ||   |  || ||||  |   ||  | || |   ||   |||  ||    | |||    ||   |                                     
TGGTCAACAAGGATCTTATCCTATCAAACTATTCTACACCTCCAACATGCCCATCATTCTTCAGAGTGCCCTCGTATCCAACTTGTACTTCATTTCACAGgtattttttttctgttacttgtcttcaatctatacagcttgcaatttctttagcaatgcgaagtatcgttgtcaatggtttcaactcattaacttcttggaattaattaaaattcaaaagacttgtcgtcttttcag

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|32849493|gb|CD989174.1|CD989174

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGT
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGT

EST: gi|6964762|gb|AW433455.1|AW433455

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTAC
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTAC

EST: gi|32836577|gb|CD976255.1|CD976255

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA

EST: gi|32932204|gb|CF037016.1|CF037016

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA

EST: gi|211341222|gb|FL045918.1|FL045918

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

EST: gi|32838942|gb|CD978623.1|CD978623

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA

EST: gi|71425883|gb|DR806950.1|DR806950

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

EST: gi|32858247|gb|CD997928.1|CD997928

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

EST: gi|32934776|gb|CF039588.1|CF039588

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTAC
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTAC

EST: gi|211338836|gb|FL045913.1|FL045913

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

EST: gi|31354346|gb|CD438703.1|CD438703

EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

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: 1015

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 941

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1188