ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTCGTCTACTACTGGCTGCACCGCGCGCTGCACCACCACTTCCTCTACTCCCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaaagcttcatttcaatagtaattaatacgccggccaaatcgacgacctgctagctgccactaatcagtcatatgcaaggtgtcctcgacctc...

Basic information

species	Zea mays
transcript	GRMZM2G066578_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G066578_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g33250.2 (Oryza sativa), 5'ss of exon 3

------------------------------------------------------------------------------CTCGTCTACTACTGGCTGCACCGCGCGCTGCACCACCACTTCCTCTACTCCCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaaagcttcatttcaatagtaattaatacgccggccaaatcgacgacctgctagctgccactaatcagtcatatgcaaggtgtcctcgacctc
                                                                               || ||||||||||| | || || ||| ||||||||||||| |||||| ||| ||||||||| ||||||||| | || |||||||| ||||| ||||| |||| | |   |  | |    || |||                                                                          
CCGGGCGGGCAACACTTACCGCTGTGGAGGACGGATGGCGCGGGGCTGATCGCCTTGCTGCATGCGGGGCCAGTGGAGTTCCTCTACTACTGGTTCCATCgtgcgttgcaccaccactttctctacacccactaccactcgcaccaccactcttcaatcgtcactgagcccatcacatgtacgtaattaattgc----cactag--------------------------------------------------------------------------

upper sequence: GRMZM2G066578_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g33250.1 (Oryza sativa), 5'ss of exon 3

CTCGTCTACTACTGGCTGCACCGCGCGCTGCACCACCACTTCCTCTACTCCCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaaagcttcatttcaatagtaattaatacgccgg---ccaaatcgacgacctgctagctgccactaatcagtcatatgcaaggt-gtcctcgacctc
 || ||||||||||| | || || ||| ||||||||||||| |||||| ||| ||||||||| ||||||||| | || |||||||| ||||| ||||| |||| | |   |  | |   |  | |    || || | |  |   |||||      |    ||    | || ||| |  | |  | | |  |     ||||    
TTCCTCTACTACTGGTTCCATCGTGCGTTGCACCACCACTTTCTCTACACCCACTACCACTCGCACCACCACTCTTCAATCGTCACTGAGCCCATCACATgtacgtaattaattgccactagaga-cggtttatcctcgaggctccaaacattacattctcttttaggcaataacctttgagcttctatattagtatcgaa---

upper sequence: GRMZM2G066578_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S364_21V6.1 (Physcomitrella patens), 5'ss of exon 3

CTCGTCTACTACTGGCTGCACCGCGCGCTGCACCACCACTTCCTCTACTCCCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaag---cagaaagcttcat-------ttcaatagtaattaatacgccggccaaat-cgacgacctgctagctgcca-ctaatcagtcatatgcaaggtgtcctcgacctc----------------------
 |  ||||||||||||| ||||| ||||| ||||| ||||||||||||  |   |||||||| || |||||||||||  |||| || |||||  || |  ||  |       ||  |||         ||| ||  || |   ||  |      ||| |  ||      |  |  ||| | ||  | |    |||  |  |  ||| |  |                       
TTTCTCTACTACTGGCTTCACCGAGCGCTTCACCATCACTTCCTCTACAACAAGTACCACTCTCATCACCACGCCTCGTTCGTAACGGAGCCCGTCTCAGgtgcggccttcgaaatttcggattgacattccatgatagtggttatactcattgaattcctcgtgtctgtgacgaccaaccaactacttgactgcgtgacggactctaattgctgggttgaattctgtgaatag

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|78076046|gb|DV504480.1|DV504480

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|76928666|gb|DV171728.1|DV171728

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|149101383|gb|EE187500.2|EE187500

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|211413211|gb|FL156318.1|FL156318

EST:     CGCTACCACTCCCNAC-ACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGA
genomic: CGCTACCACTCCC-ACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGA

EST: gi|211418301|gb|FL156340.1|FL156340

EST:     CGCTACCACTCCCACCCAC-ACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CGCTACCACTCCCACC-ACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|148956804|gb|EC902698.2|EC902698

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|76018388|gb|DT945558.1|DT945558

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|148999701|gb|EE036698.2|EE036698

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|78091933|gb|DV520307.1|DV520307

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|93015094|gb|EB640614.1|EB640614

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|211520982|gb|FL156352.1|FL156352

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|211418299|gb|FL156338.1|FL156338

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|148930973|gb|EC873493.2|EC873493

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

EST: gi|89757801|gb|DY687247.1|DY687247

EST:     CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCT                         CCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA
genomic: CCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAA

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: 52

CTCGTCTACTACTGGCTGCACCGCGCGCTGCACCACCACTTCCTCTACTCCCGCTACCACTCCCACCACCACGCCTCCATCGTCACCGAGCCAATCACCTgtaagcagaa ... ttttgtgcagCCGTCATCCATCCATTTGCTGAGCTCGTGGCGTATGAACTATTGTTCTCAATCCCATTGATTGTGTGCACCTTGAACGGAACTGCTTCAATTATTGCATT

Block sizes: 12 (upstream exon), 38 (downstream exon)
Score: 1