RetrogeneDB ID: retro_rnor_1505

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:88037595..88038008(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snap23
• Ensembl ID: ENSRNOG00000050552
• Aliases: None
• Description: synaptosomal-associated protein 23 [Source:MGI Symbol;Acc:MGI:109356]

Sequence

>retro_rnor_1505
TTAGTCTTTGTATCTCAGGATGCAGGAATAAACACCATCACTATGATGGACGAACAAGGGGAACTACTAAATCACATAGA
AGAAGGCATGGACCATATAAATAAAGACATGAGAGAAGCAGAGAATACTTAATAGAACTCAACAAGTGTCCCCTCGGTGT
CTGCCCTTGTAATAGGACAAATAACTTTGAGTCTGGAAAGAACTATAAGGTAACATGGGGAGATAGCGGAGACAACTCAC
CCAGCAATGTGGTATCTAAGCAACCAGTCCAGATAACAAATGGTCAGCCTCAGCAAACTACAAGCGCAGGCACCGGTGGA
TACATTAAACATATAACTAATGATGCCAGAGAAGATGAGACCAGAGAGAACCGCATTCAAATGGAGAGCAACCAAGGCAG
CATAAGGAACATG

Alignment

ORF - retro_rnor_1505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.57 %
• Parental protein coverage: 66.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAIESQDAGIKTITMLDEQGEQLNRIEEGMDQINKDMREAEKT-LTELNKCCGLCVCPCNRTKNFESGKN
          L...SQDAGI.TITM.DEQGE.LN.IEEGMD.INKDMREAE.T.L.ELNKC..L.VCPCNRT.NFESGKN
Retrocopy LVFVSQDAGINTITMMDEQGELLNHIEEGMDHINKDMREAENT<LIELNKC-PLGVCPCNRTNNFESGKN

Parental  YKATWGDGGDSSPSNVVSKQPSRITNGQPQQTTGAASGGYIKRYTSSSKENDGSKNMVTEGSIEGNNKNM
          YK.TWGD.GD.SPSNVVSKQP..ITNGQPQQTT.A..GGYIK..T....E.....N.....S..G...NM
Retrocopy YKVTWGDSGDNSPSNVVSKQPVQITNGQPQQTTSAGTGGYIKHITNDAREDETRENRIQMESNQGSIRNM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	2.44 RPM
SRP017611_kidney	0.07 RPM	16.75 RPM
SRP017611_liver	0.00 RPM	4.84 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1505 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1505 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505 , retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,