ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatgtgttctggcaaaatcgacatgcttcatgcacatttctggatgcagtgcgtgaaaggttcatgtctgtgttccatcgatttcttagcaaac...

Basic information

species	Zea mays
transcript	GRMZM2G020976_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 2

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatgtgttct----ggcaaaatcgacatgcttcatgcacatttctggatgcagtgcgtgaaaggttcatgtctgtgttccatcgatttcttagcaaac
|| ||||||||||||||||||||||||| || |||||||| || ||||| || ||||||||||| |||||||||||||||||     ||| |     |    | ||   |   |          |  |   |   |   |||     | ||  | |       |   | ||  | |     
TGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAGgtacttctcatgtccccttggatggactctggaaagtctggctttgctgttatgttgtgcaagtgtgcattacacatttacacatgaataacttgcttgt----

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 5'ss of exon 2

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatgtgttctggcaaaatcgacatgcttcatgcacatttctggatgcagtgcgtgaaagg--ttcatgtctgtgttcc--atcgatttcttagcaaac--
| ||  | ||||| || ||||||||||| |||||||| ||  | |||||||| |||| ||||||||| ||| ||||||||   |||   | ||||| |  |        ||| ||   ||   | |    |     | || |   || || | |    |||  ||  |  | | |   ||   
TTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAGgta---gat---tcctggccatcttttttcttttcttggcaatcaattgccttatataatcaaggtgtttgattttttcactcctcatgcaactttaattgaaaat

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|71298002|gb|DR784970.1|DR784970

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|31353270|gb|CD437627.1|CD437627

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|78115509|gb|DV533897.1|DV533897

EST:     TCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCCACGCTCCTTCCG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: TCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATC-ACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|71767957|gb|DR965894.1|DR965894

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|71420101|gb|DR805011.1|DR805011

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|93282589|gb|EB674853.1|EB674853

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|78076866|gb|DV505300.1|DV505300

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|31355902|gb|CD440259.1|CD440259

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|148947455|gb|EC892886.2|EC892886

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

EST: gi|74233567|gb|DT641481.1|DT641481

EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         AGGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

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: 48 (upstream exon), 48 (downstream exon)
Score: 87

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 152

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 184