ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA

Basic information

species	Zea mays
transcript	GRMZM2G044137_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 1

---------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtgaa---ttttcctgtgatgttgat--tggtctcccgtt----ggtttcgat--ctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA
               |  ||  || |   |  ||||  | |   | |||| || || ||      |   |||   || ||||||  |  |||| ||   ||    ||||  |      ||||||||||||||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||   
gtaaggttcctgatcgattgcgcctccctccccctcc-tcgtcgcgctctcccgctgcgcatctcaccatttcgttgcgatgtttttgctggtttctgattggtgggttgtggcgatgatgcagAAGAAGAGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACT---

upper sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 3'ss of exon 1

-----------gtatgaacc-ccaagcaacctcagttg-gtcctctcttccacttcggggtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA
           ||||           | | || | ||    | ||||| | | |   | |      | | | | || ||| ||| | |   |||| ||| ||  |   ||||||||||    ||| | |||||||||||||||    || ||||||||||||||||||||||| || |||||||||||||| |||||||  ||  | | ||   
gtacggacatcgtattcgttgttccccgatcttattttcaacttctctacgattcaagagatgtaatgcatttcattttgtttgattttgtgttgttttggaaat-cacagAAGAAGACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCT---

upper sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 1
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 1

---------------------------------------gtatgaaccccaagcaacctcagttggtcctctcttccacttcggggtg------aattttcctgtgatgttga---ttggtctcccgttggtttcgatc-tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA
                                       ||   |||    ||   || | || |  |   || ||||      ||||      || |    |  | | ||||   | |||| | ||     || |  |    ||||||||||| |   |||| |||||||  |   |||  ||||||||||||||| ||||||||||| |||||||||||||||  ||| ||||| ||||||       
gtgcgtagggcagatgcagtagcaaaactagccgcagccgtcaaaacggagagtcgccgccgtcg--ctggtcgtccagcgtaaggtggctacaaaatcaaatcaggtattgaacctcggtcgcgcgcgtactttgtgcacccgcagAAGAAGACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGG---

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|149089950|gb|EE179239.2|EE179239

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|211067927|gb|FL140853.1|FL140853

EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|60355557|gb|DN222530.1|DN222530

EST:     CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|60394375|gb|DN227245.1|DN227245

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|9824981|gb|BE575183.1|BE575183

EST:     GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCG                         AAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGC
genomic: GTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGC

EST: gi|60338522|gb|DN205495.1|DN205495

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|15100298|gb|BI396089.1|BI396089

EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|89251915|gb|DY623701.1|DY623701

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|31406277|gb|CD485009.1|CD485009

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|31441073|gb|CD510504.1|CD510504

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|211067924|gb|FL140850.1|FL140850

EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|60347030|gb|DN214003.1|DN214003

EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|67023955|gb|CO452704.1|CO452704

EST:     CCCATCGCCGCCAGTGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|60341097|gb|DN208070.1|DN208070

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|27575973|gb|CA998667.1|CA998667

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|76013092|gb|DT940262.1|DT940262

EST:     CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|211065202|gb|FL140848.1|FL140848

EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|211065201|gb|FL140847.1|FL140847

EST:     CCCATCGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

EST: gi|60357629|gb|DN224602.1|DN224602

EST:     CCCATCGCCGCCAGCGGCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGAAG                       
genomic: CCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTC---Ggtatgaaccc ... tatgcaga

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: 57

CGCAGCCCGCAGTCGCTTGCGCGCAGCAGCACTTCGCACCGCCGCCCCATCCCATTGCCGCCAGTGTCTGCTCGATCCGATGGCTCCCACGAAGAAGTCGgtatgaaccc ... tatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 34

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtgaattttcctgtgatgttgattggtctcccgttggtttcgatctatgcagaagAAGAGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCA