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

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC

Basic information

species	Zea mays
transcript	GRMZM2G063492_T01
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 10

gtatgtcttttctgg-attcagtttttctagcaaaaattatggttcttacttcttaca-----ttatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
||||||  | ||||  | |||||||| || ||||   || |||||  |  |   |  |     |||||||||    || ||||| ||||   | ||| || |||||| |||||||| |||||||| |||||||| |||||||| || || ||||||||||||||||||||| |||||||||| || |||||||||||||| |||
gtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacagGCACACTTTTGCTACTTTATCTTTCATTGCTGAAATTTTTCTATTTCTCTATGTTGGGATGGATGCACTGGACATTGAAAAATGGAAATTAGCTAGCAGC

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 8

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
||| ||    |       ||  ||    ||  |     | | ||  ||||  | | | ||  || ||| |||  |          |||| || |||||||||  |||||| ||||| ||||||||||| ||||| ||  | ||||||||||| |||||||||||||| || || || ||||||  | | |  |||   
gtacgtgaaattcttcaacacattcatgagacatgtacaagattgctactaatgatactactta-actgattaat----------ttccctgctgcagGCATGTTTTTGCCACTTTGTCATTCATTGCTGAAATCTTTATCTTCCTCTATGTGGGGATGGATGCATTAGATATAGAAAAGTGGCGAATTGTAAGTCAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 9

gtatgtcttttctggattcagtttttcta-gcaaaaattatggttcttacttctta--cattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
            |   |  | || ||| |  ||   |||| ||    |||    ||   | ||   |||||| ||      |||   ||||| ||  ||||||||  |||||| ||||| ||||||||||| ||||| ||  | ||||||||||| |||||||||||||| || || || ||||||  | | |  |||   
-----------gtacgtgaaattcttcaacacattcatta-ggcatgtacaagatagctactaatgatactacttaactgattttaatttccctgccgcagGCATGTTTTTGCCACTTTGTCATTCATTGCTGAAATCTTTATCTTCCTCTATGTGGGGATGGATGCATTAGATATAGAAAAGTGGCGAATTGTAAGTCAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 10

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
|||||||||  ||  ||  || ||| ||  ||| |  || |     |   ||  |   |||| ||||  |   |  |||||   |     | |||||||||| |||||||||| || || ||  |||| || || ||  | ||||| |||||||| |||||||| ||||||||||| || |||||||| |  |||   
gtatgtctt--ctaaat--agatttcct--caagatatacgcacactg--tccaagtctatgcatacctaa-acatatttttcatccaactcttgcagGCATTCTTTTGCAACCTTGTCTTTTGTTGCTGAGATCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAATGGAAATTTGTCAGTGAT

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 9

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaa---ttgctgattttctctttcca-------tgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
   | | |  ||| ||     || ||| ||| ||  ||||   |    ||  ||   ||  |  || |||   |  || ||||  | | |  |       |||| ||| ||| ||||||||||| | |||||  ||   ||||  ||  | ||||| |||||||| |||||||| ||||||||||| |||||||  || | ||||   
--gtatatcctctagac---attcttcaagctaag-ttatatatggatctatttgggttgggggtagtaacactgtctaatttgatttattaaaacttgttgttacagACATGCTTTTGCAACTCTCTCATTTGTTCTTGAAACCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAGTGGAGGTTTGTTAGTGAT

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 9

gtatgtcttttctggattcagtttttctagcaaaaat---tatggttcttacttcttacattatgtatactaattgctgatttt---ctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
   | | |  |||  |   | || ||| ||| ||  |   ||||| |||   |       | |      ||||||    || ||   ||  || | |||| ||| ||| ||||||||||| | |||||  ||   ||||  ||  | ||||| |||||||| |||||||| ||||||||||| |||||||  || | ||||   
--gtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgc-tgttacagACATGCTTTTGCAACTCTCTCATTTGTTCTTGAAACCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAGTGGAGGTTTGTTAGTGAT

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 10

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
||||||||| |    |  ||| ||| ||     || |||||     |   ||  |   |||| ||||  |   |  |||||| |    | | |||||||||| |||||||||| || |||||  |||| || || ||  | ||||| |||||||| |||||||| ||||||||||| || |||||||| |  |||   
gtatgtcttct----aaacagatttcctc----aagttatgtacactg--tccaagtctatgcatacctaa-acatattttcacccaac-tcttgcagGCATTCTTTTGCAACCTTGTCATTTGTTGCTGAGATCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAATGGAAATTCGTCAGTGAT

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 10

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
       | | |    || ||||| ||   |      |  | ||   ||||  ||| |       | ||  |  |||||||   |||| |||   ||||||||| ||||||||||| |||||  |||| || |  ||  ||||| | |||||||| |||||||| ||||||||||| ||||||| ||  |  |||  |
------gtatgcaaactttagtttctccgccttttgctgagattaacactttctacctcccaatgattatcttatgatttt---tttcgatgaaacagGCATACCTTTGCAACTTTGTCATTTCTTGCGGAGACATTTATTTTCTTGTATGTTGGAATGGATGCCTTGGACATTGACAAGTGGAGATCCGTGAGTGAC

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6

gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaa-ttgctgattttctctttcc-atgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
       |  | ||   ||  |||| ||    ||||  |   |||  |  | || |||  |  ||||| | || ||   | |   ||| | |||   ||||||| | ||||| ||||| || ||  | || || | |||  |||||||||| ||||| ||||||||||||||||| ||||| |||| ||| |  |||  |
------gtaatatgacctccatttt-ctcttgaaaacaa--attcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 9

-----------------gtatgtcttttctggattcag--tttttctagcaaaaattatggttcttacttcttaca-ttatgt-atac-taattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
                   || | || ||   ||   |      | |    |  ||| |  || || |     | | ||||||   |  || || ||| || | | | |   | ||||||||||||||||||||| ||||| ||  || | || |||||  | ||||| |||||||| || ||||| ||||||||||||||||||    | |  || | |
gtaagctaaatcttcagaaatattttctcaaaatctggaacccattttcttattattttattttttcccaaaaaaaattatgttgcatgtattttctgtttctgtttatgatttttgcagGCATACTTTTGCAACGTTATCTTTTGTTTCTGAGATTTTTATCTTCCTGTATGTTGGTATTGATGCCTTGGACATTGAGAAGTGGCGGGTTGTAAGCAAC

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 9

gtatgtcttttc-tggattcagtt-------tttctagcaaaaattatggttcttacttcttacattatgta--tactaattg-----ctgattt--tctctttccatg------ttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
|||||| ||||| || |  || ||       ||| | |  |  |||    || ||| |||  | | || ||   ||||   ||     ||| |||  | ||| || ||          ||||||| ||||||| || || |||||  | || || |||||| | ||||| |||||||| |||||||| |||||||||||||| |||| ||| |  || |  
gtatgtattttcctgaaagcaattggaacattttttggtcaggatttatatttttatttcaaaaaataggtcattactggctgtatgcctgttttaatttctgtctataaaatttccacagGCATGCTTTTGCGACCTTGTCATTTGTAGCTGAGATTTTCATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAGAAATGGAGATTTGTGAGCAAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 10

gtatgtc---ttttctggattcagtttttctagcaaaaattatggttcttacttcttac-attatgtatactaa---------ttgctgatttt----ctctttccatgt---tgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
||||||    | | | |||       | |  |     | | ||  |  || | | || | |  ||||  | |||         |||||||| ||     |||| |||  |   ||||||||| ||||||| || || |||||  |||| ||||||||  | || || |||||||| |||||||| |||||||||||||| |||| ||| |  |||   
gtatgttaattatccaggaagtgaagtattgaaattcattcatcttcattccattttgccaaaatgttgattaaactgtgatgttgctgatgttacagttcttaccaaatgtttgcagGCATGCTTTTGCGACATTGTCATTTGTTGCTGAAATTTTTATCTTTCTATATGTTGGCATGGATGCCTTGGACATTGAGAAATGGAGATTTGTAAGTGAT

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S233_97V6.1 (Physcomitrella patens), 3'ss of exon 9

-gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctc-tttccat--gttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC
 | | |     | |   ||   ||||  |  |||         ||  || | || |   ||||      || |  |  |   | |  ||| ||   |||||||||||||||||||||  | || |||||||||||  ||||| | || || |||||||||||||| ||  ||||||| || || |||| |    ||     |
agcaggggcactattctttttattttattttcaacggacccaatttataatgctgag--tatgagcgtcaacttgtagtgaacgcgcttctattgattgcagGCATACTTTTGCAACAATGTCGTTCATTGCAGAGGTTTTCATATTTCTGTATGTTGGGATGGACGCGGTGGACATAGACAAATGGAGACGGACTCAATCC

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|18963600|gb|BM660526.1|BM660526

EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTC
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTC

EST: gi|71311178|gb|DR791899.1|DR791899

EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTCTTCCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA

EST: gi|89106454|gb|DY576671.1|DY576671

EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA

EST: gi|18963602|gb|BM660527.1|BM660527

EST:     GCATAATGTGCCAGAAAGTTCTAGGGTTCCCCCCAA                         GCATACTTTTGCACCTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
genomic: GCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA

EST: gi|67026824|gb|CO455573.1|CO455573

EST:     CACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGGTTAC-ACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTTCTCTA
genomic: CACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGG-TTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 168

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 298

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 311

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC

                                  ttttctctttccatgt  CT-rich tract
             attatgtatactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA