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

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC

Basic information

species	Zea mays
transcript	GRMZM2G060999_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G060999_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g32350.1 (Oryza sativa), 3'ss of exon 3

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttg--------tggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC---
                                                                                                     | ||| ||  | | |   ||| ||| |     | |  || |||| ||||  ||  ||| |||||||| |         |||||||     ||||||||||||||| || ||||| || |||||||| ||||| |||   || ||| |||||||||||||||| || ||||||||||||| |||| |||| ||||   
---------------------------------------------------------------------------------------------------gtaagtagtacaattgtttgtag-ttattgccgctttcttttactggagaaaaatgttaaattgcatccataattccatatggttatacacatcagGTTCTGGATGAGATCCACCAACAGTCTGCTGCCTTATCCTCA---AGGCCATCGTTTTCTTCAATTGGGTCCGTTCCTGCTCCAAAGGAGGTTGTCGAGCGTC

upper sequence: GRMZM2G060999_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G35490.1 (Glycine max), 3'ss of exon 3

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagat-taatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC---
                                                                                                     | || | |   |     |||| | |  | ||   ||  || | |  | ||  |||| || ||| ||  ||||   ||||    | |||||||||||||||||||||| ||||||   |  ||||| ||     | ||  |  | || || || || ||||||||||| || |  ||  |||| ||     
---------------------------------------------------------------------------------------------------gtaagttcaatgtacggtgttagctgttctggtg--gtcattcattttataattatac-aagttgaatatttgtacatattttaattagGTTCTGGATGAAATTCACCAGCAATCTATGGTTTTATCTTCTC---GCCCTTCTGTGTCATCTATCGGTTCTGTTCCTGCACCTAATGAAGTTGTGGAATCCT

upper sequence: GRMZM2G060999_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G35060.1 (Glycine max), 3'ss of exon 5

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC---
                                                                                                     | || | |   |     ||||  |  |  |  ||  | |   |  | ||  |||| || ||| ||  ||||   ||||    | |||||||||||||||||||||| |||||||  |  |||||   |||  | ||  |  | || || || || || |||||||| || |  ||  |||| ||     
---------------------------------------------------------------------------------------------------gtaagttcaatgcactgtgttag--ttgttctggtggccatcgttttataattatac-aagttgaatatttgtacatattttaattagGTTCTGGATGAAATTCACCAGCAATCTGTGGTTTTATC---ATCTCGCCCTTCTGTGTCATCTATCGGTTCCGTTCCTGCACCTAATGACGTTGTGGAATCCT

upper sequence: GRMZM2G060999_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G08260.1 (Glycine max), 3'ss of exon 6

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC---
                                                                                           ||  |  |||  || ||  | |  |  |  | ||  |  | ||     | |||  | |    ||||   |       ||||   ||||    | ||||||| |||||||||||||||||||||| ||  ||||| ||     | ||| |  | ||||| ||||||||||||||||| || |  ||  |||| ||     
------------------------------------------------------------------------------------------gtaattttaaa--gtgctgtttagttactctggtttctgatgat--cactaact--atatttttactgtttgaatcttttgtacatattttaattagGTTCTAGATGAAATTCACCACCAATCTGTTGTTTTATCTTCCC---GCCCATCTGTATCTTCTATTGGATCTGTTCCTGCACCTAATGATGTTGTCGATTCCT

upper sequence: GRMZM2G060999_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0087g00420.t01 (Vitis vinifera), 3'ss of exon 3

gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC---
                                                                                      | |     ||| |  |     |  |   ||  | |  ||   |||| | |  |||  | |   |  |   ||| ||| ||  || |  |||| || |  |||||||||||||||||||||| |||||||  |  ||||||||     ||||  |  | ||||| ||||| ||||||||||||||||  ||  |||| ||     
-------------------------------------------------------------------------------------gtgatgctaatatattattatattttgtgatggtcacttttccagtattttctttgtatcattcaata---taagttgaattttttt--ttat-acctatagGTTCTGGATGAAATTCACCAGCAATCTGTGGTCTTATCGTCCC---GACCTTCTGTATCTTCTATTGGTTCTGTTCCTGCTCCAAATGAAGTTGTAGAATCTT

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|71448740|gb|DR829790.1|DR829790

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|110195219|gb|EC877116.1|EC877116

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|148999940|gb|EE037001.2|EE037001

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTTTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|71299450|gb|DR785731.1|DR785731

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|101398514|gb|EB821130.1|EB821130

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|78544416|gb|DV621914.1|DV621914

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGATCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|71325678|gb|DR799524.1|DR799524

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|71771687|gb|DR969624.1|DR969624

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|5847602|gb|AW000681.1|AW000681

EST:     CAAGGGCTAGCATATCAAGAATTGGTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|101398512|gb|EB821129.1|EB821129

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|60400728|gb|DN233535.1|DN233535

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|5525666|gb|AI861559.1|AI861559

EST:     AGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA
genomic: AGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

EST: gi|20315421|gb|BQ169270.1|BQ169270

EST:     CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAG                         GTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGATCA
genomic: CAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 125

CAACTGCAGAACAGGTAGTCGACAAGGCAATCCTGATGAAGAAACTAGCACAAGGGCTAGCATATCAAGAATTGTTATGTTAGCAGAAGCACTATTTGAGgtacgttgtg ... ttactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC

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

Block sizes: 44 (upstream exon), 39 (downstream exon)
Score: 25

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

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC

                     tactaac  putative branch site (score: 49)
                                             ttactttc  putative PPT
                                          ttattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttgtgcaaatatacgtactgcctctgtccaaaaaatgattgtaattctcgcttttaataagtcaatcaatatcaagtttgatcaaatagatacaaaaggtactaataatatcattagattaatagtaatgttcttgactgaagaaggatactaacttgcatccttgtggttattactttcagGTTCTGGATGAAATTCACCACCAATCTGCTGCGTTATCGTCATCAAGACCAGCGTTTTCTTCAATTGGATCTGTTCCTGCTCCAAGGGAGATTGTTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT