RetrogeneDB ID: retro_mmus_2236

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:37599426..37599951(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081093
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prelid1
• Ensembl ID: ENSMUSG00000021486
• Aliases: Prelid1, 2610524G07Rik, Preli
• Description: PRELI domain containing 1 [Source:MGI Symbol;Acc:MGI:1913744]

Sequence

>retro_mmus_2236
GAGGTGACCCCCGACCAGAAGCTACTGTCCCGGAGACTCCTGACCAAGACCAACAGGATGCCACGTTGGGCAGAGTGACT
GTTTCCTGCCAACGTTGCTCACTCCGTGTACATCCTGGAGGACTCTATAGTGGACCCCCAGAATCAGACCATGACCACCT
TCACCTGGAACATCAACCATGCCCGGCTGATGGTGATGGAGGAATGATGCGTTTACTGTGTGAACTCTGACAATACCGGC
TGGACCGAAATCTGTCGGGAAGCCTGGGTCTCCTCTAGCTTATTTGGCATCTCCAGAGCTGTTCAGGAATTTGGTCTTGC
CTGGTTCAAAAGCAATGTGACCAAGACAATGAAGGGCTTTGAATACATCCTGGCCAAGCTACAAGGTGAGGCCCCTTCCA
AAACCCTTGTTAAGACAGCCAAAGAGGCCAAAGAGAAAGCAAAGGAGACCGTACTGGCAGCTACAGAGAAGGCCAAGGAC
CTGGCCAACAAGGCCGCCACCAAGCAGCAGCAGTGGCAGCTCGTA

Alignment

ORF - retro_mmus_2236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.29 %
• Parental protein coverage: 80.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVTPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERC
          EVTPDQKLLSRRLLTKTNRMPRWAE.LFPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMV.EE.C
Retrocopy EVTPDQKLLSRRLLTKTNRMPRWAE*LFPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVMEE*C

Parental  VYCVNSDNSGWTEIRREAWVSSSLFGVSRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETA
          VYCVNSDN.GWTEI.REAWVSSSLFG.SRAVQEFGLA.FKSNVTKTMKGFEYILAKLQGEAPSKTLV.TA
Retrocopy VYCVNSDNTGWTEICREAWVSSSLFGISRAVQEFGLAWFKSNVTKTMKGFEYILAKLQGEAPSKTLVKTA

Parental  KEAKEKAKETALAATEKAKDLANKAATKQQQRQLV
          KEAKEKAKET.LAATEKAKDLANKAATKQQQ.QLV
Retrocopy KEAKEKAKETVLAATEKAKDLANKAATKQQQWQLV

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
SRP007412_brain	0.00 RPM	36.96 RPM
SRP007412_cerebellum	0.00 RPM	29.44 RPM
SRP007412_heart	0.03 RPM	12.86 RPM
SRP007412_kidney	0.04 RPM	53.88 RPM
SRP007412_liver	0.00 RPM	55.19 RPM
SRP007412_testis	0.09 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2236 was not detected

EST

No EST(s) were mapped for retro_mmus_2236 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_94648	136 libraries	435 libraries	475 libraries	21 libraries	5 libraries

The graphical summary, for retro_mmus_2236 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2236 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236 , retro_mmus_2394, retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178, retro_rnor_2305, retro_rnor_637, retro_rnor_995,