ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgttcttccctcatgcaataaagttattatgatatatcaaattttacgctttgcaaatttatagatacttgataattaaaaataatcaccttc...

Basic information

species	Zea mays
transcript	GRMZM2G161337_T03
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G161337_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g15780.4 (Oryza sativa), 5'ss of exon 9

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgttcttccctcatgcaataaagttattatgatatatcaaattttacgctttgcaaattt---atagatacttgataattaaaaataatcaccttc-
                   || |||||||| ||||| |||||||||||||| || |||||||||||  | ||||||||||| ||||||||||| || ||||||||||| ||||||    || |  | ||   ||  |  | ||   | || ||  | |||  ||| |    |   || |   |  || |  ||      || | 
-------------------GTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACGgttaggctcttcttct---atactgtgaaacaatggttctgtactca-ttatataccttggcaatgttgcgtcattattatttccttcagcattccagtctgca

upper sequence: GRMZM2G161337_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G23680.1 (Glycine max), 5'ss of exon 9

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgttcttccctcatgcaataaagttattatgatatatcaaattttacg----ctttg-caaatttatagatacttgataattaaaaataatcaccttc
                   || |||||||| || || ||  | || || ||| | ||||| |||||| | || |||||||||||||||||||||||||| || | | |  | |  |   ||   | ||| ||   |  || | |   | | |  |    || || || | ||||   |  || |         | ||| | |   
-------------------GTCTCCAAACCGGGTTCTGTTCAAGTTGAAAAGCTTATGAATATTGAGCGCTATTCCCATGTTATGCACATCAGCTCAACAgt-aagttcctttagcaaaatatga-aaatttggaaatatgtgtttgaatatgtgaaaactatgtcacaattatcctttttttactgcatgtcacaattatc---

upper sequence: GRMZM2G161337_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G03260.1 (Glycine max), 5'ss of exon 9

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgttcttccctcatgcaataaagttattatgatatatcaaattttacgctttgcaaatttatagatacttgataattaaaaataatcaccttc--------
                   ||  | |||   || ||||| || ||||| ||| | ||||| |||||| |||| |||||||| |||||||| ||||||||||| ||    || |    | |      |  |||| | || | |   ||  |  |  || |  || |  ||   |   |   ||  ||||||  | |   |         
-------------------GTTGCAAAAAGTGGTTCAGTTAAAGTGGAAAAGCTTATGAATATTGAGCGATATTCCCATGTCATGCACATAAGCTCAACGgtgagaaccttttcttgttagtatcgagtgttagt-tggtgttctaacatagatactatttaattgcatctttctgtttcaaaaaaaaatgttgattatttattgtag

upper sequence: GRMZM2G161337_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 5'ss of exon 9

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctg--ttcttccctcatgcaataaagttattatgatatatca------aattt-----tacgctttgcaaatttatagatacttgataattaaaaataatcaccttc--------------------------------------------------
                   || |||||||| || || ||||  || || ||| | ||||| |||||| | ||||||||||| |||||||||||||| ||||| |   |   || |    | ||  |  || | | || | | ||||||       ||||      |   | |  ||    || ||| || || ||  | |     |     |                                                   
-------------------GTGTCCAAACCTGGTTCTGTGACTGTTGAAAAGCTCATGAATATTGAGCGCTACTCCCATGTCATGCACATCAGCTCCACGgtaaatataaattttgtaataatttatcaaggctgtttttacatatcatcataggatttgataacataatataaaaggcaatggatgctggagaaacatattagtttgttattcagtataacaactgattcattactaataaaatccttaaccggctttgcag

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|7227817|gb|AW566458.1|AW566458

EST:     ATCAGCTCAACG                         GTTAGTGGGCAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: ATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|71762476|gb|DR960413.1|DR960413

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|211345790|gb|FL266263.1|FL266263

EST:     ATACTCCCATGTTATGCACATCAGCTCAACG                         GTYAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: ATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|149103558|gb|EE288957.2|EE288957

EST:     CCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: CCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|8930541|gb|BE225305.1|BE225305

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|4887265|gb|AI677364.1|AI677364

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|37392136|gb|CF633315.1|CF633315

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|211345792|gb|FL266265.1|FL266265

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|548048|gb|T25248.1|T25248

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|166617705|gb|EG206258.1|EG206258

EST:     CTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: CTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|71761802|gb|DR959739.1|DR959739

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|60357763|gb|DN224736.1|DN224736

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|213175359|gb|FM190077.1|FM190077

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|148939087|gb|EC883495.2|EC883495

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|60398523|gb|DN231339.1|DN231339

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|149000181|gb|EE037320.2|EE037320

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|5713996|gb|AI943981.1|AI943981

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

EST: gi|13178556|gb|BG349814.1|BG349814

EST:     AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG                         GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT
genomic: AGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCT

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: 248

GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgt ... atgtttgcagGTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 912

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1562

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 276

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGACTGCGGCTTGATAGGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACGgttaggctgttcttccctcatgcaataaagttattatgatatatcaaattttacgctttgcaaatttatagatacttgataattaaaaataatcaccttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA