ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATGGACTATGCATTTGAGTTCATCATCAACAATGGCGGAATCGACACCGAGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttgcttccatagtttttccttgattttccaaagaccagcagcgtcatttttacttactgctgatcttgtgtgttgggtccatctattgcag

Basic information

species	Zea mays
transcript	GRMZM2G166281_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G166281_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S49_32V6.1 (Physcomitrella patens), 5'ss of exon 2

GATGGACTATGCATTTGAGTTCATCATCAACAATGGCGGAATCGACACCGAGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttgcttccatagtttttcc---ttgattttccaaag-accagcagcgtcatttttac--ttact-gctgatcttgtgtgttgggtccatctatt-gcag-------------------------------------------------------------------------------------
 ||||| ||||| ||||| ||||||||||| ||||| |||||||| |||||| |||| ||||| |||||||  || || || |  |||||||    |||||||   | |  |    |  ||||  |   |||| || | |    |       |   ||||  ||  | | | | | ||| |||| | |  | |  | | || ||||                                                                                     
TATGGATTATGCGTTTGATTTCATCATCAAAAATGGTGGAATCGATACCGAGGAGGACTACCCCTACAAGGCAACTGATGGCCAATGTGATGAGGCCAGGgtaaactctaatgttttgattttctccatttgaattactacgttatgttttacaaaatttcaacggtgattagtttatcatgtgaggtatggcattttgttcgcagatttagccagaatttggcattcatttgcatcttggtgttgttcgatttctctcagaatcttattagtgacgattctctcttgcag

upper sequence: GRMZM2G166281_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 2

GATGGACTATGCATTTGAGTTCATCATCAACAATGGCGGAATCGACACCGAGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttgcttccatagtttttccttgattttccaaagaccagcagcgtcatttttacttactgctgatcttgtgtgttgggtccatc-tattgcag------------------------------------
 |||||||||||||| ||||| || ||||| ||||| || || ||||| ||||||||||| |||||||||| ||  || || ||||| ||||     || |||  | |          ||| || | |    |  || |  |   ||   | | ||| | | | |  | ||   || |   |  |  |||  || | |                                     
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctagcggttatttcat----tcacacaatctcccat--ttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag

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|16920327|gb|BM074601.1|BM074601

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|13515985|gb|BG518261.1|BG518261

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGTTTTTGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|32923037|gb|CF027849.1|CF027849

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATATACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|18170436|gb|BM340276.1|BM340276

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGAAGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|32923298|gb|CF028110.1|CF028110

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATATACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|71444254|gb|DR825304.1|DR825304

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|18172588|gb|BM347976.1|BM347976

EST:     AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGAAGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

EST: gi|211384516|gb|FL378678.1|FL378678

EST:     AGAAGGATTACCCTTACAAGG-CACGGACGGACGATGTGATGTCAACAGG                         AAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC
genomic: AGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAAC

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: 642

GATGGACTATGCATTTGAGTTCATCATCAACAATGGCGGAATCGACACCGAGAAGGATTACCCTTACAAGGGCACGGACGGACGGTGTGATGTCAACAGGgtattttttg ... tctattgcagAAAAACGCGAAGGTTGTCACTATTGACAGCTACGAAGATGTACCAGCGAACGATGAGAAGAGTCTGCAGAAGGCAGTTGCAAACCAGCCTGTCAGTGTCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4179

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4515