ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagatttgattctaaattaaacgagcagactattttgcagatacatttcttcgctgattgttggcactgacttccctgcgtag

Basic information

species	Zea mays
transcript	GRMZM2G129513_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G129513_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 5'ss of exon 8

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagatttgattctaaatta------------------------aacgagcagactattttgcaga-tacatttcttcgctgattgttggcactgactt-ccctgcgtag
|||||||||||||| ||||||||||||||||||||||||||  ||||||||||||||||||| || || |||||||||||||| |||||  | ||||                        ||  |    ||  || ||  |  ||| ||| ||   |  || ||     ||| || | ||| ||||
CTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAGgtgaagatatgattagatattactggctttctattgtaatacttccaattattgtacctttctgtggggtacttttgtttattc-ttattactgatgatttgctctgagtag

upper sequence: GRMZM2G129513_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 8

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaa-gatttgattctaaattaa----acgagcagactattttgcagatacatttct-tcgctgattgttggcactgacttccctgcgtag
||||| || ||||||||||| || ||||| ||||| ||||| || || ||||||||||| || ||||| ||||||||||  || | ||||||   ||||    | ||  |||  || ||     ||  ||  | |    || |  |     | | || | |  |   
CTGGCTCTCAAAGCAGGTGTCTTCTATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAGgtgatcgaatagattctgtcttaagaacatgaatagataatattctttctattttcttgtaaaggaatactcagtataattttcatcag---

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|110219294|gb|EC901192.1|EC901192

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|78089786|gb|DV518160.1|DV518160

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|32916975|gb|CF021787.1|CF021787

EST:     TGACAAAGTATCAAACGTGACTATTTGGGGGAACCCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAATTTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAAGTATCAAACGTGACTATTTGGGGGAA-CCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|211195515|gb|FL441324.1|FL441324

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|13198702|gb|BG354504.1|BG354504

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|211398041|gb|FL283723.1|FL283723

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGACTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|148971653|gb|EE022376.2|EE022376

EST:     TGACAAAGTATCAAACGTGACTATTTGGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAAGTATCAAACGTGACTATTT-GGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|148928691|gb|EC873304.2|EC873304

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|211395432|gb|FL283722.1|FL283722

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGACTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|211129427|gb|FL299354.1|FL299354

EST:     GGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: GGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|211195516|gb|FL441325.1|FL441325

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|30706123|gb|CD059034.1|CD059034

EST:     AAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAACGCCCAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: AAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|74239371|gb|DT647285.1|DT647285

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|13558383|gb|BG549739.1|BG549739

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|13490961|gb|BG517725.1|BG517725

EST:     TGACAAANNNNNNNNACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAA-GTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC

EST: gi|30705491|gb|CD058800.1|CD058800

EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTC

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: 44 (upstream exon), 48 (downstream exon)
Score: 38

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 583

Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 3