ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctggagattcttctattttgctcctgtatcattttcagatgaaatggtttggtacttagaaattgattttcaaacttcactacag

Basic information

species	Zea mays
transcript	GRMZM5G835235_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 5

ATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctggag-attctt--ctattttgctcctgtatcattttcagatgaaatggtttggtacttagaaattgattttcaaacttcactacag
|| ||||| ||||| |||||||| |||  ||  ||||| || |||||||||||||| |||||||| |||||||||||||||| ||   || ||  | |||   |||   || ||   ||  ||       | ||  ||||   ||||||| ||  ||||||    |||
ATTTGTAGGGCATTAGCTTACATCCATAATAGCATCGGAGTTTGCCACAGAGATATCAAGCCACAGAATCTTCTGgtatgcttgaatgttgttacccattcatctcaaataccaccctcttatt------tctgtaactttataattgatgtttgaacttctaatcag

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|213187425|gb|FM190443.1|FM190443

EST:     CGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTNNNG                         GTGAACCCACACACCCACCAACTTAAAATATGTGACTTTGGTAGTGCAAA
genomic: CGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTT-CTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAA

EST: gi|67039601|gb|CO465856.1|CO465856

EST:     ATGGTACAATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACC-ACACACCCACCAGCTTAAA-TATGTGACTTTGGTAGTGCAAAA
genomic: ATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA

EST: gi|213187001|gb|FM192338.1|FM192338

EST:     ATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATNNNTCTG                         GTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAA
genomic: ATCGGTGTCTGCCACAGAGATATTAAGCCACAAAAT-CTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAA

EST: gi|32830913|gb|CD970591.1|CD970591

EST:     ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA
genomic: ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA

EST: gi|32830394|gb|CD970072.1|CD970072

EST:     ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACCCACACTCCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA
genomic: ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA

EST: gi|32831124|gb|CD970802.1|CD970802

EST:     ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA
genomic: ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA

EST: gi|211480778|gb|FL342573.1|FL342573

EST:     ATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA
genomic: ATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA

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: 265

ATATGTAGAGCATTGGCTTACATTCATGGTACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCATACATCTGCTCGCGATACT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307