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

gtaattatactgattgcaaaacgcatagatacaactttgtgtcactatactcggcgcttctgataataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA

Basic information

species	Zea mays
transcript	GRMZM2G092112_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 6

gtaattatactgattgcaaaacgcatagatacaactt-tgtgtca-ctatactcggcgcttctgataataatgtac-agGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
|||||||| |  | |  | |    |||   ||| ||  ||| | | |  |  |       |||||||    | |   ||||||| |||||||||||||||||||| |||||||||||||| || || |||||||||||||||||||| ||||||||||||||  |
gtaattatgcaaaatttacag-atatac-cacatctcatgtttgatcctttgttaataaatctgatacccttttcttagGTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGA

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7

---------------------------------------------------------------gtaattatactgattgcaaaacgcatagatacaac-tttgtgtcactatactcggcgcttctgataataatgtac-agGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
                                                                || | |   ||       || |   |  |  | | ||||||| | | ||     |   | || || |  | |   |||| ||||||||||||||||||||||| ||||| |||||||| || ||||||||||||||||||||||| |||  |||||||||  |
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgta----acaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6

---------gtaattatactgattgcaaaacgcatagatacaactttgtgtcactatactcgg----cgcttctgataat-----------aatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
           |||| |  | ||    ||  | |||  |     |    ||    ||| |        | || ||||  |           |||||  ||||||| |||||||||||||||||||| ||||| || |||   || ||  | ||||| |||   || ||||||   || || || ||
ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttgattatgatgttcacttttatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6

-------------------gtaattat--actgattgcaaaacg--catagatacaactttgtgtcactatactcggcgcttctgata-ataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
                    ||||  |  ||||| | |        | ||| |  ||  |||   |  |      |  | | ||  ||   |||||  ||||||| |||||||||||||||||||| ||||| || |||   || ||  | || || |||   |||||||||   || || || ||
tttatcctagagaattttcttaatcttgaactgaatcctttttcttcctagtttgaatattgaagctttgattatgatgttactattatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6

gtaa-ttatactgattgcaaaacgcatagatacaactttgtgtcact-atactcggcgcttctgataataa----tgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
|||| || | ||  || |     | ||   || ||  | ||    || ||| |     ||    |  || |    | |  ||||||||||||||||||| |||||||| ||||| || ||    || ||  | ||||| |||  | | ||||||   ||||| || ||
gtaagttttgctactttcc--ttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 6

gtaa-ttatactgattgcaaaacgcatagatacaactttgtgtcact-atactcggcgcttctgataataa----tgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA--------------
|||| || | ||  || |     | ||   || ||  | ||    || ||| |     ||    |  || |    | |  ||||||||||||||||||| |||||||| ||||| || ||    || ||  | ||||| |||  | | ||||||   ||||| || ||              
gtaagttttgctactttcc--ttgtatgtttataatctcgttctgctcatatttttgtctaaacaacatgaaacatatttagGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAGTATCCTTATAACT

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6

----------gtaattatactg---attgcaaaacgcata----gatac-aactttgtgtcactatactcggcgctt--ctg----ataataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
             | ||||| |   |||  | ||  | |     ||||       || | |||       |  | ||  |||     |   ||  || ||||||| |||||||||||||||||||| ||||| || |||   || ||  | ||||| |||| ||| ||||||   ||||| |||||
tatgtcatcaactagtatacagcttattttagaatactttccttgatattggaactgaggcaccgactaagaagtttatctgtactgtggaaacatatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCA

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|31360578|gb|CD444935.1|CD444935

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTC
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTC

EST: gi|67020672|gb|CO449421.1|CO449421

EST:     AATCGGAACAATAA-TAACTTTCNGCCTAG-ACGTCTTTCTA-TGTANAG                         GGTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: AATCGGAACAATAAATAACTTTC-GCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|86471374|gb|DY237744.1|DY237744

EST:     ACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: ACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|74242756|gb|DT650670.1|DT650670

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAAT-CTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|29545091|gb|CB605269.1|CB605269

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|67014170|gb|CO442919.1|CO442919

EST:     TAATCGGAACAATAAATAACTNTCGCCTAGGACGTCTTTCTAATGTANAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|7238063|gb|AW573435.1|AW573435

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|24767878|gb|CA403013.1|CA403013

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

EST: gi|40303501|gb|CK347888.1|CK347888

EST:     TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAG                         GTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG
genomic: TAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTG

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: 172

GAAGCGTACTAATGTTCTCAATGATGCATTCTATATATCACATGATGGAGTAATCGGAACAATAAATAACTTTCGCCTAGGACGTCTTTCTAATGTAGAGgtaattatac ... taatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cgcatagatacaactttgtgtcactatactcggcgcttctgataataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA

                                    ttctgat  putative branch site (score: 182)
                                         ataataatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatactgattgcaaaacgcatagatacaactttgtgtcactatactcggcgcttctgataataatgtacagGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT