ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtcaaccatctgtttccttatttcttaacattggcaattccaatatgtagttgtgtttgacttgtcaagacgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAACAGTCAAGATGAGGTTCTCAAGTTGCTAGAGAAGGACGCTTTCCTATAG

Basic information

species	Zea mays
transcript	GRMZM5G800734_T02
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g33810.5 (Oryza sativa), 3'ss of exon 6

gtaagtc--aaccatctgtttccttatttcttaacattggcaattccaatatgtagttgtgtttgacttgtcaa-----gacgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAACAGTCAAGATGAGGTTCTCAAGTTGCTAGAGAAGGACGCTTTCCTATAG
||||||   ||||| || |||| |         |          | |  |      |||||  | |||||   |     || ||   |||||||| |||||||||||||||||| |||||||||||||| ||||| || ||||  || |||||||| |||||| |||| |||| ||||||||||||||| 
gtaagtttaaaccagctatttcatctaaaaccgagtcgatttgatgccctgctagtttgtgcctaacttgatgaaaattgatgaccccagCACGCCCCAGAATCTGGACGGGAAGACCCCCATCGAGGTGGCCAAGCTGAACAACCAGGATGAGGTCCTCAAGGTGCTCGAGATGGACGCTTTCCTATAA

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|14245007|gb|BG842945.2|BG842945

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|20513053|gb|BQ280239.1|BQ280239

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|12972249|gb|BG267888.1|BG267888

EST:     ATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: ATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|60346930|gb|DN213903.1|DN213903

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|30087804|gb|CB886010.1|CB886010

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTACAAAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAGCTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|32823312|gb|CD963034.1|CD963034

EST:     GATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: GATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|13381712|gb|BG458267.1|BG458267

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|60355695|gb|DN222668.1|DN222668

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|113704194|gb|EE681698.1|EE681698

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|74034821|gb|DT535312.1|DT535312

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|21809483|gb|BQ667801.1|BQ667801

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|33091656|gb|CF051650.1|CF051650

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|14243333|gb|BG840971.2|BG840971

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|4610100|gb|AI600939.1|AI600939

EST:     AGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: AGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|13515751|gb|BG518027.1|BG518027

EST:     GTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: GTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|21394198|gb|BQ538628.1|BQ538628

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|31558361|gb|CD527573.1|CD527573

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|4621551|gb|AI612384.1|AI612384

EST:     ATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: ATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|213182765|gb|FM187299.1|FM187299

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|5030685|gb|AI714879.1|AI714879

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|17921593|gb|BM259244.1|BM259244

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|17921594|gb|BM259245.1|BM259245

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|60338870|gb|DN205843.1|DN205843

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|37398879|gb|CF636759.1|CF636759

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|60399415|gb|DN232227.1|DN232227

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|37390740|gb|CF632604.1|CF632604

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|78179376|gb|DV549749.1|DV549749

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAGCTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|33468092|gb|CF245141.1|CF245141

EST:     GAAGGAATGTGTGGATCTTCTGTTGAAGTATGG-GCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: GAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

EST: gi|109179476|gb|EC380017.1|EC380017

EST:     TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGT                         CACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA
genomic: TATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAA

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: 395

TTGATGCCCTAGATAAGAACAAGAACACTCCGTTGCACTATGCTGCTGGGTATGGTCGGAAGGAATGTGTGGATCTTCTGTTGAAGTATGGTGCTGCTGTgtaagtcaac ... acgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAACAGTCAAGATGAGGTTCTCAAGTTGCTAGAGAAGGACGCTTTCCTATAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 484

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttaacattggcaattccaatatgtagttgtgtttgacttgtcaagacgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAACAGTCAAGATGAGGTTCTCAAGTTGCTAGAGAAGGACGCTTTCCTATAG

                 aatatgta  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaaccatctgtttccttatttcttaacattggcaattccaatatgtagttgtgtttgacttgtcaagacgattacagCACGCTCCAGAATCTGGACGGGAAAACCCCCATCGAGGTTGCCAAACTCAACAGTCAAGATGAGGTTCTCAAGTTGCTAGAGAAGGACGCTTTCCTATAG

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