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

gtgagtgcattttcatacttgggttaatcttgtcacttgtgtgccagtgttcacgtagatgtgtaaaaatggtctacctgaatgaaagttccatagagaaatgacaatgttaacttattgttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG

Basic information

species	Zea mays
transcript	GRMZM2G472770_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G472770_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 3

gtgagtgcattttcatacttgggt---taatcttgtcacttgtgtgccagtgttcacgtagatgtgt------aaaaatggtctac--ctgaatgaaagttc--------------catagagaaatgac--aatgt-taactt---attgttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG
||||||| ||| | | ||| | ||   ||||  | ||||    | | ||   || |  ||||| | |      | ||||| | |||  | ||   |||  ||              |||   ||||| |   ||||| ||||||   | | ||  ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||| |||| |||||| ||||| || |||||||||||||||
gtgagtgtattctgaaactcgagtaactaattctttcacaaagg-gtcaccatttatttagatatatactgtcataaatgttgtacaacagagaaaaaaatctctactggaacatgcattaggaaattatgaaatgtctaactttccaatatttattcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGCCACCACAAACTTACTGTTCAGTTTTTAGAGGCATCTGCAGCACAAGATAGGAAATTG

upper sequence: GRMZM2G472770_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g07470.1 (Oryza sativa), 3'ss of exon 3

gtgagtgcattttcatacttgggt--taatcttgtcacttgtgtgccagtgttcacgtagat---gtgtaaaaatggtctacctgaatgaaagttc--------------catagagaaatgacaatgttaact---tattgttgt---------ttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG
||||||| |||||   ||||| ||   ||  |   | |    ||   ||||||||| |||||   |    |||||  | |||||||| |||||||               |||   ||||| |  ||  ||| |   || | || |         ||||||||||| || ||||||||||| |||||||||||||||||||| |||||||| || ||||| || |||||||||||||||||||| ||||| |||||||||
gtgagtgtattttggaacttgagtaacaaattctccgcggaggttgaagtgttcacatagataaagaacgaaaatattatacctgaaagaaagttgtctactagaacatgcattatgaaataaatataataattgtctacttttctgatatgtcattcagGTGGGTGGGCGTAGGTGATGCCACAGGGGATTATCCATTTAGCCACCACAAACTCACCGTCCAGTTTTCAGAGGCGTCTGCTGCTCAAGACAGGAAATTG

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|211349626|gb|FK991789.1|FK991789

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGG
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGG

EST: gi|211352036|gb|FK991805.1|FK991805

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211349624|gb|FK991787.1|FK991787

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352030|gb|FK991799.1|FK991799

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211354437|gb|FK991814.1|FK991814

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211349625|gb|FK991788.1|FK991788

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352034|gb|FK991803.1|FK991803

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211349631|gb|FK991794.1|FK991794

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211349629|gb|FK991792.1|FK991792

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211349628|gb|FK991791.1|FK991791

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211354436|gb|FK991813.1|FK991813

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352032|gb|FK991801.1|FK991801

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352033|gb|FK991802.1|FK991802

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352029|gb|FK991798.1|FK991798

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352037|gb|FK991806.1|FK991806

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAA

EST: gi|211352038|gb|FK991807.1|FK991807

EST:     CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAG                         GTGGGTTGGTGTAGG
genomic: CGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGG

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: 104

AAGAGTTTAGGGCAAGTACTTCAGCTGATTCTATGACCAAGCATCAATCACGTTATGTGTTGCAAGTAATAAAATACGTAACAAACCATCCTGACAACAGgtgagtgcat ... gttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 70

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tacctgaatgaaagttccatagagaaatgacaatgttaacttattgttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG

                                 tgttaac  putative branch site (score: 93)
                                              ttgtttc  putative PPT
                               aatgttaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcattttcatacttgggttaatcttgtcacttgtgtgccagtgttcacgtagatgtgtaaaaatggtctacctgaatgaaagttccatagagaaatgacaatgttaacttattgttgtttcagGTGGGTTGGTGTAGGTGATGCTACAGGGGATTATCCATTTAGTCACCACAAGCTTACCGTTCAATTTTCAGAGGCGTCTGCTGCCCAAGATAGGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC