ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataacttttccactattcagtcattcttcaaagtaggcagttgctttttaggtaaatttgtataattgtatggaaacatcacctcactgccttaacc...

Basic information

species	Zea mays
transcript	GRMZM2G442404_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G442404_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 7

GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataacttttc-----cactat-tcagtc-----attcttcaaagtaggcagttgctttttaggtaaatttgtataattgtatggaaacatcacctcactgccttaacc-----------------------------------------------------------------
|||||||   ||| ||| ||  |||||||||| ||||| ||||| || || ||||||||||| |||||||||||||||||||     |     || ||| |||  |     |   ||| || |   || |         | |   | ||||  |||| |   || |||||| | | || |||  |                                                                  
GAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAGgtaataaaccaccaagcacattatctcaacctgaaaacgattcgaatttctcaatgaaaccactgctgcttatgtagcattgaaca-aagcatcactttattgtcttctctgtctgatctgggtatacatttttaatgattgctaaattctctgataattctgtttaccaaaatag

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|37398527|gb|CF636579.1|CF636579

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|4776156|gb|AI665159.1|AI665159

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|211024205|gb|FL472254.1|FL472254

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|32863266|gb|CF002948.1|CF002948

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|37375819|gb|CF624378.1|CF624378

EST:     GCCTGGTTCTCG-TAAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: GCCTGGTTCTCGCT-AGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|32925505|gb|CF030317.1|CF030317

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|148973759|gb|EE024892.2|EE024892

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|71307033|gb|DR789670.1|DR789670

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|37374878|gb|CF623839.1|CF623839

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

EST: gi|149051712|gb|EE155827.2|EE155827

EST:     AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG                         GAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG
genomic: AATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGG

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: 36

GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAGgtaataactt ... tgaaaaaaagGAAGCCGTTTCCCTTGGCAAATCAGAGGACACGCCAGAGTCTGCAGCTCGGAAATTGACAGAGATCGCTTATTCTCGTGGCAGCGCTGACAATATCACGT

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 21

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 18