RetrogeneDB ID: retro_mmus_2816

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:41306401..41306747(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Cdc42
• Ensembl ID: ENSMUSG00000006699
• Aliases: Cdc42, AI747189, AU018915
• Description: cell division cycle 42 [Source:MGI Symbol;Acc:MGI:106211]

Sequence

>retro_mmus_2816
GTTGTCAGTGATGATGCTGTTGATAAAACATGTTTAGTGATATCCTATTCAGTGAATAAATTTCCATAAAAATATGTACC
TGTACCAGCTGTTTTGGACAACTATGGAGTCACTCTAATGATTGGTAGGGAGCCATACACTCTTGGACTTTTTGATACTT
TAGGACAAGAAGATTATGACAGACTATGACTAGTAAGTTATCCCCAGACAACTGTTTTTTTCTAGTATGATTCTTGTGAC
CTCTCCATCCTCATTTGAAAATGTGAACGAAAAGTGGGTGCCTGAGATTATTCACCACTGTCCAAAGACTCCTTTCTTGC
TTGTTGGGACTCAAATGGGGCTCAGG

Alignment

ORF - retro_mmus_2816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 59.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVGDGAVGKTCLLISYTTNKFPSEYVPT--VFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQT
          VV.D.AV.KTCL.ISY..NKFP..YVP...V.DNY.VT.MIG.EPYTLGLFDT.GQEDYDRL...SYPQT
Retrocopy VVSDDAVDKTCLVISYSVNKFP*KYVPVPAVLDNYGVTLMIGREPYTLGLFDTLGQEDYDRL*LVSYPQT

Parental  DVFL-VCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLR
          .VF......V.SPSSFENV.EKWVPEI.HHCPKTPFLLVGTQ..LR
Retrocopy TVFF>SMILVTSPSSFENVNEKWVPEIIHHCPKTPFLLVGTQMGLR

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	215.97 RPM
SRP007412_cerebellum	0.00 RPM	169.26 RPM
SRP007412_heart	0.00 RPM	99.83 RPM
SRP007412_kidney	0.00 RPM	164.91 RPM
SRP007412_liver	0.00 RPM	103.20 RPM
SRP007412_testis	0.00 RPM	39.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2816 was not detected

EST

No EST(s) were mapped for retro_mmus_2816 retrocopy.

TSS

No TSS is located nearby retro_mmus_2816 retrocopy 5' end.

Lab

retro_mmus_2816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2816 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus	ENSECAG00000019180	1 retrocopy	retro_ecab_11,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Gorilla gorilla	ENSGGOG00000024439	5 retrocopies	retro_ggor_1932, retro_ggor_2057, retro_ggor_2303, retro_ggor_2593, retro_ggor_2695,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Mus musculus	ENSMUSG00000006699	3 retrocopies	retro_mmus_2816 , retro_mmus_2995, retro_mmus_3170,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,