ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCGCATCGCGCGGTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTAGGCGCCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatcccccgccccacttcttcctctcttgctgtttaccaggtctacgccggtccggtctcgatgtttgaatcccccgtcgtgagtcgattgtttccttggttttcgcag

Basic information

species	Zea mays
transcript	GRMZM2G107540_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107540_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g51200.1 (Oryza sativa), 5'ss of exon 1

CCGCATCGCGCGGTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTAGGCGCCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatcccccgccccacttcttcctctcttgctgtttaccaggtctacgccggtccggtctcgatgtttgaatcccccgtcgtgagtcgattgtttccttggttt-tcgcag
||||||||| || |||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||||||||||| ||||  |||  |  || || |||   | |  |    | ||| |  || ||  || ||       |||||    ||  ||| ||     ||  ||  |||  ||||||
CCGCATCGCCCGCTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTCGGCGCCGGCGCCCCCGTCTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaaaccccatcccttcccctcccgctcgatccgcgtg--ggatcttc--cgatctcgtgtcc---cccgaatcgtgtgttctga-tcacccattggctgtgttaatcgcag

upper sequence: GRMZM2G107540_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv07s0104g00970.t01 (Vitis vinifera), 5'ss of exon 1

CCGCATCGCGCGGTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTAGGCGCCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatcccccgccccacttcttcctctcttgctgtttaccaggtctacgccggtccggtctcgatgtttgaatcccccgtcgtgagtcgattgtttccttggttttcgcag
||| ||||| || | |||||| ||||| |||||||| || || || || || || |||||||| || ||||||||||| ||||||||||| || || |||||      |        |  ||  |   ||| | | | |   || |  |  | || |     ||   |||||      |   | |     | |       ||||       
CCGAATCGCCCGTTTCCTCAAAGCCGGAAAGTACGCCGAACGTGTCGGGGCTGGCGCTCCCGTTTATCTCTCCGCCGTTCTCGAGTACCTTGCGGCTGAGgttggtgtcttatgtgatcgttggttgtttgtt-tctgctttgtttg-gttgctcggaaaatgag--ttgaacgtattgaaattaaaaactcggagatgaggtt-------

upper sequence: GRMZM2G107540_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ38642 (Selaginella moellendorffii), 5'ss of exon 1

CCGCATCGCGCGGTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTAGGCGCCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatcccccgccccacttcttcctctcttgctgtttaccaggtctacgccggtccggtctcgatgtttgaatcccccgtcgtgagtcgattgtttccttggttttcgcag
  | ||||| || | ||||||||| |||||||| || ||||| || || ||||| ||||| || ||| |  ||||||| |||||||| || ||||||||||||       |  |  |    || |   ||   | ||    ||  |      ||      |||| |  | |     |  |  || || |||  | | |   |         
AAGGATCGCTCGATTCCTCAAGGCGGGCAAGTATGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTACATGGCCGCCGTGCTCGAGTATCTAGCCGCCGAGgta--tgtgtgatcttcgcgctcatgggtttagggttcttgggcttttctttgtggcagatcgaagagtaa-----cgattttgtgt-gatgatctacccag---------

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|26456550|gb|CA828133.1|CA828133

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|26559803|gb|CA832038.1|CA832038

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|78544756|gb|DV622254.1|DV622254

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|211392088|gb|FL250788.1|FL250788

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|113650513|gb|DW808138.1|DW808138

EST:     CTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|211392085|gb|FL250785.1|FL250785

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|211392091|gb|FL250791.1|FL250791

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|211392086|gb|FL250786.1|FL250786

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|87155479|gb|DY400268.1|DY400268

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|20802962|gb|BQ294012.1|BQ294012

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|20336981|gb|BQ172611.1|BQ172611

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|211392090|gb|FL250790.1|FL250790

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

EST: gi|22819198|gb|BU499288.1|BU499288

EST:     CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAG                         GTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC
genomic: CCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATC

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), 49 (downstream exon)
Score: 55

CCGCATCGCGCGGTACCTCAAGGCCGGCAAGTACGCGGAGCGCGTAGGCGCCGGGGCTCCCGTGTACCTCTCCGCCGTCCTCGAGTACCTCGCCGCCGAGgtaatccccc ... gttttcgcagGTGCTGGAGCTGGCCGGGAACGCTGCTCGGGACAACAAGAAGAACCGGATCGTGCCGCGCCACATTCAGCTGGCGGTGCGGAACGACGAGGAGCTGAGCA

Block sizes: 31 (upstream exon), 45 (downstream exon)
Score: 36

Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 32