ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...cttcatagcgaagtttatagccagcaaaaaaaaaagaagtgttattcttaatgcatgatctgatatcacatttatacacctaatgacaccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA

Basic information

species	Zea mays
transcript	GRMZM2G099754_T02
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g02830.1 (Oryza sativa), 3'ss of exon 5

-----------------------------------------------cttcatagcgaagtttatagccagcaaaaa------aaaaag------aagtgttattctta-atgcatgatctgatatcacatttata----cacctaatg-----acaccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA
                                               ||  ||||||   ||      || |||||       | ||||      ||||| ||| |    |||||   |||| | |  |  ||  |    || || |||     | ||| | |  |||||||||||||||||| | ||||| || |||||||| || || ||||| || || ||| |||| ||||| ||||| ||||||||||| ||||||||||||||
gtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagtttctgtt-ttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGCAGGGA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 5

----------------------------------------------------------------------cttcatagcgaagtttatagccagcaaaaaaaa---aagaagtgttattctta-atgcatgatctgatatcacatttata----cacctaatg-----acaccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA
                                                                           |  | | |||  | | ||  || ||||    |  ||||  ||| |    |||||   |||| | |  |  ||  |    || || |||     | ||| | |  |||||||||||||||||| | ||||| || |||||||| || || ||||| || || ||| |||| ||||| ||||| ||||||||||| |||||||| |||||
gtactgtcctcgttttatcttttttaaattttctacatttttttctgagtagcgttgttacccttcatcaaaatgtgaccaggttatttgtcaaaaagaaaagtttaccaagtaatatgcaagtatgcagtttctgtt-ttgcccttgcaatttcatctgatgtatatatacctattgggcagGTCACTTGACTGCTAGAAGTGATGTCTACAGCTTTGGTGTTGTCCTTCTTGAACTCTTGACTGGGCGTAAGTCCATCGACAAGTCACGGCCCAGTAGGGA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ35779 (Selaginella moellendorffii), 3'ss of exon 4

---cttcatagcgaagtttatagcc-agcaaaaaaaaaagaagtgttattcttaatgc--atgatct---gatatcacatttatacacctaatgaca--ccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA
   |||  |      |||  |   | ||  ||          || |  |   |  |    | |||||   || |         | |  || ||| |   |||  |||||||||||||||||  || |||| || || || ||||| ||||| ||  |||||||| |||||||||||||    || || ||||||   ||||| ||| | ||
gtactttttcttctcgttcttgctcgagtgaagctctctttcgtttcttcagtcgtttcgacgatcttgcgagagtgagagcttgcgactcatgcctttccggctttgcagGTCACTTGACACCTAGGAGCGATGTATATAGCTTTGGCGTTGTTTTGCTGGAGATCCTGACGGGGCGACGATCCATGGACAAGAACCGGCCGAGCGGCGA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ10730 (Selaginella moellendorffii), 3'ss of exon 4

---cttcatagcgaagtttatagcc-agcaaaaaaaaaagaagtgttattcttaatgc--atgatct---gatatcacatttatacacctaatgaca--ccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA
   |||  |      |||  |   | ||  ||          || |  |      |    | |||||   || |         | |  || ||| |   |||  |||||||||||||||||  || |||| || || || ||||| ||||| ||  |||||||| |||||||||||||    || || ||||||   ||||| ||| | ||
gtactttttcttctcgttcttgctcgagtgaagctgtctttcgtttcttcagccgtttcgacgatcttgcgagagtgagagcttgcgactcatgcctttccggctttgcagGTCACTTGACACCTAGGAGCGATGTATATAGCTTTGGCGTTGTTTTGCTGGAGATCCTGACGGGGCGACGATCCATGGACAAGAACCGGCCGAGCGGCGA

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|78089252|gb|DV517626.1|DV517626

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|149096770|gb|EE182550.2|EE182550

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|4628292|gb|AI619166.1|AI619166

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|22489206|gb|BU049116.1|BU049116

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|60357259|gb|DN224232.1|DN224232

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|78089253|gb|DV517627.1|DV517627

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|30705953|gb|CD058982.1|CD058982

EST:     TGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: TGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|76011906|gb|DT939076.1|DT939076

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|18383934|gb|BM417134.1|BM417134

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|148991732|gb|EE033300.2|EE033300

EST:     CGGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: C-GGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|6601822|gb|AW256263.1|AW256263

EST:     ACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCNCTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|60398709|gb|DN231525.1|DN231525

EST:     CCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGATTCGGCGTGGTCCTGCTGG
genomic: CCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|67032695|gb|CO461444.1|CO461444

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCCGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|6637068|gb|AW261340.1|AW261340

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

EST: gi|149038591|gb|EE155518.2|EE155518

EST:     ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCG                         GTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG
genomic: ACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 23

TTTGGCCTCGCAAAAGATGGCCCTGAAGGTGATCAGACGCATGTGTCGACACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcct ... gaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA

Block sizes: 33 (upstream exon), 47 (downstream exon)
Score: 11

Block sizes: 49 (upstream exon), 28 (downstream exon)
Score: 6

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttaatgcatgatctgatatcacatttatacacctaatgacaccgaatttgcagGTCACTTGACTGCTCGGAGTGACGTGTACAGCTTCGGCGTGGTCCTGCTGGAGCTCCTGACGGGGCGCAAGTCGATCGACAAGTCGCGGCCCAGCAGGGA