ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata...

Basic information

species	Zea mays
transcript	GRMZM2G128771_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G14390.1 (Glycine max), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtata-gttgtaatcattgcatgac-accagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata-
|||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||| ||  | || ||||||||  | |||||||   |  |    ||| ||||        |||||   | |  | |||    |   ||   || |  ||||    |||   |||   |  || | || | 
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTAgtgagtt-ttatatgttcttttatataccactttcattatctaattaacaggattttttatggatctt--ttcctattttctcatgacataacttttccaaat

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G38110.1 (Glycine max), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatg-cata-----
|||||||||||| || || |||||||| ||||| |||||||||||||| || || ||||||||||| ||  |||| ||||||||| |||||||||     |      ||  ||  ||   |    |   |  ||  | ||  |  | | | | ||  |||   |  | | | ||    | | ||| ||||     
GGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCAgtgagtg---tagtggtttttcattttttctaaatgtcagtttcattatctaattagctgtgttct--ttctgaatcttccgagattt-tctcatgtcataattct

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G31200.1 (Glycine max), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata------
|||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||||||  | || ||||||||  | |||||||     ||     || ||    | | || ||   || |      | ||     |||       |  ||   |||   |||   |  || | || |      
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTAgtgagttttataag----ttataccaatttcattatctaataat--tgacaggatttttctggatctttatcaattttctcatgacataacttttccaaattattt

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G02040.1 (Glycine max), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtc-actcaaaaaccttgtatagttgtaatca-ttgcatgacaccagctggtccgatctttcctggttc---cagacttccggtgaacaatgttatgcata
|||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||| || ||||| || |||||| |||||||||| | |       | | | | ||      || || |||      |  || |  | ||||||  | |     |||| || |     |||  ||| |     
GGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCAgtgagtctagttgtttttcattttttgtaactgccagtttcattgtctaatttgctgtgttctttctggatctttacagattttctcacgacatagttct-----

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata
||||||||| ||||| || || || |||||||| || ||||| |||||||| || |||||||||||  | ||||| || |||||||||||| ||||        |||||     |||    || |||  |  ||||  ||  |  |   | |  ||  | ||      |  |      ||||       
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtcc-------accttt----gtttctctctttgatt--caccttcttttttgtgttcttatgtgttcaa----tcaatactttgtgttgcag---

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactc-----aaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata------------------------------------
||||||||||||||||||||| ||| | ||||| || ||||| || ||||| || ||||||||||| ||  |||| ||||||||  | ||| || |          | ||| ||  |   ||   ||||  |  |  | |      || | ||||   | || |||    ||  |   ||  ||| | || | |                                    
GGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAAgtaaggcttcttctgtgagaacttttcagctttaccatcaaagt-ttcctcttttgtgtacaatctacacaggatccttctttttgc--aaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatag

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 5'ss of exon 3

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata---
||||||||| || || || || |||||||||||||| ||||||||||| || || ||||| ||||| ||| |||||||||||||    ||||||| | | |  ||    | |||  |  | |  ||  | || ||||     | | | | | |    | |   | ||   ||   |||  | | | |     
GGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAAgtgagt-agtaattaaatcagcataaattgagttttttga-gaaaccattgatttctaacatgcactttactgaatttgttgtacccaa-ataagggaagcag

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 5'ss of exon 5

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggtt-ccagacttccggtgaacaatgttatgcata
||| ||||| ||||||||||||||||||||| | ||||| ||||||||| |||| || || || || |||||||| |||||||| |||||| ||| | |        ||   ||      | || ||  |     ||  ||    | |   |     ||   |||     ||     | || | |    |
GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCAgtaagt-atttgtttgattttcttacccaagagcactgtgtctttacacttgagttgttgcgtaagatttgttagaaggatggcctctactggtgtatcaa

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|149095335|gb|EE180972.2|EE180972

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

EST: gi|211449139|gb|FL349634.1|FL349634

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGGAACACCTCAAAGTGGATCGATGAAGTGCGCACC
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTG-AACACCTCAAAGTGGATCGATGAAGTGCGCACC

EST: gi|37387848|gb|CF631126.1|CF631126

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

EST: gi|37379915|gb|CF626729.1|CF626729

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

EST: gi|40335969|gb|CK370039.1|CK370039

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

EST: gi|211481374|gb|FL368109.1|FL368109

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

EST: gi|211492534|gb|FL462461.1|FL462461

EST:     AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA                         ATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG
genomic: AAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCG

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: 20 (upstream exon), 30 (downstream exon)
Score: 1

GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcact ... atccatacagATAGACAGTCCTTCCTGAACACCTCAAAGTGGATCGATGAAGTGCGCACCGAGAGAGGTGGCGATGTGATAATCGTGCTCGTTGGCAACAAAACTGATCT

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 9

Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 6

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 177

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCAgtgagtcactcaaaaaccttgtatagttgtaatcattgcatgacaccagctggtccgatctttcctggttccagacttccggtgaacaatgttatgcata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaacc