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

...atgcataacagctgatggcaattgtgatctccttcttcatgaaatgttattttctctgatggacacataaattgacctcccactttgtaattcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT

Basic information

species	Zea mays
transcript	GRMZM2G468260_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G468260_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 4

atgcataacagctgatggcaattgtgatctccttcttcatgaaatgttattttctctgatggacacataaattgacctcccactttgtaattcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT------------
||   | |||||||  || |  | |  | |   || |    ||| | | |||||  |      |        ||   | |    || |||| |   |||||| |||||||||||||||||||||||||  || | |||| || ||          | ||||||||||| |||      ||| || ||||||| ||||| |            
atagctgacagctgtcggaatctattttgtttctcctttccaaacgatgttttccttctaactcttgattgatgttttgctttcttctaatcctccgcagAAAATGGAGTTTGACGAGACAACATAATTGTCAGACTGGCCTGTAT-------TTCTTGGATTAACAACCCTC-----ATGGCAATCTGAAAGTACAGGTGGTCTAGGCCAC

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|149029755|gb|EE154767.2|EE154767

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|67028741|gb|CO457490.1|CO457490

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|8103125|gb|AW927785.1|AW927785

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|18179901|gb|BM381111.1|BM381111

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|78178991|gb|DV549364.1|DV549364

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|93012750|gb|EB638270.1|EB638270

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|211295922|gb|FL460683.1|FL460683

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|50337985|gb|CO533111.1|CO533111

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|7844561|gb|AW787783.1|AW787783

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTC
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTC

EST: gi|71756382|gb|DR954319.1|DR954319

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|71444055|gb|DR825105.1|DR825105

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

EST: gi|211285705|gb|FL480404.1|FL480404

EST:     GTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTCTGTGGAAAG                         AAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT
genomic: GTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCAT

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: 48 (upstream exon), 46 (downstream exon)
Score: 58

TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtt ... ttcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 116

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttattttctctgatggacacataaattgacctcccactttgtaattcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT

                        aattgac  putative branch site (score: 116)
                   acataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcataacagctgatggcaattgtgatctccttcttcatgaaatgttattttctctgatggacacataaattgacctcccactttgtaattcaatgcagAAGATGGAGTTTGACGAGACAACATAATCCTCTGGCTGGACTCTACACCATGGCCCATGGATTAACAAACCTTCTCATATGACATTCTGAAAATACAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA