ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCGTGTCGGAGGAGATCCAGTCTAACGTGGTGGTGCTCACCGACTATTCCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttcccgcgattctgttccccaccccccgcttattcagtgctgcgagccttgatatgcatcccgattagcgattagtctgggccatagagttta...

Basic information

species	Zea mays
transcript	GRMZM2G414569_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G414569_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 1

GTGCGTGTCGGAGGAGATCCAGTCTAACGTGGTGGTGCTCACCGACTATTCCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttcccgcgattctgttccccaccccccgcttattcagtgctgc-----gagccttgatatgcatcccgattagcgattagtctgggccatagagttta
||||||||| |||||||||||||| ||||||||||||||| |||||||  || |||||||||||||||||||||  || ||||||||||||||||||||||||    | ||| |  ||||   |  | | | |  |  ||||  || |||     |   |||    ||  |    |||   |  | | ||  |   |||  |   
GTGCGTGTCCGAGGAGATCCAGTCCAACGTGGTGGTGCTCGCCGACTACGCCCTCATGTACGAGTCCCACCCCTCCTCCCACCCCACCATCGCCGTCAAGgta--attccccacatttctagccgtctctcgcttcggattctatgatgcagtgaggcgcttccgttgttttggaatttttggatgggctccgatctaggtt---

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|5846833|gb|AI999916.1|AI999916

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|60352391|gb|DN219364.1|DN219364

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAATACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|91869882|gb|EB400589.1|EB400589

EST:     AGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTTTACAGTT
genomic: AGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|37422451|gb|CF648936.1|CF648936

EST:     CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGC
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGC

EST: gi|60394039|gb|DN226909.1|DN226909

EST:     CACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAATACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|91869884|gb|EB400590.1|EB400590

EST:     AGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: AGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|5325020|gb|AI783211.1|AI783211

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|211528538|gb|FL329337.1|FL329337

EST:     CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|40286941|gb|CK327333.1|CK327333

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|40287068|gb|CK327460.1|CK327460

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|18174124|gb|BM349512.1|BM349512

EST:     GCACCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: GCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|61119681|gb|DN560642.1|DN560642

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAG
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAG

EST: gi|6020792|gb|AW065720.1|AW065720

EST:     CCATCATGTTCGAGTCCCACCCCTATTCGCATCCCACCATCGCCGTCAAG                         GTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT
genomic: CCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTT

EST: gi|6020682|gb|AW065490.1|AW065490

EST:     ATCATGTTCGAGTCCCACCCCT-TTCGCATCCCACCATTNCGCCGTCAAG                         GTTACTTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGT
genomic: ATCATGTACGAGTCCCACCCCTATTCGCACCCCACCA-T-CGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTAC-TTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGT

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), 48 (downstream exon)
Score: 47

GTGCGTGTCGGAGGAGATCCAGTCTAACGTGGTGGTGCTCACCGACTATTCCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttc ... ctctgtgcagGTTACTTCACCATATGGGAACACCTTGCATCACAGTGAGAATTCTACAGTTGGTCAATTTGCATTCACAACCGCAGAAGCTGGAAACTACGTTGCATGCT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 78

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGTGTCGGAGGAGATCCAGTCTAACGTGGTGGTGCTCACCGACTATTCCATCATGTACGAGTCCCACCCCTATTCGCACCCCACCATCGCCGTCAAGgtatcgcttcccgcgattctgttccccaccccccgcttattcagtgctgcgagccttgatatgcatcccgattagcgattagtctgggccatagagttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgct