RetrogeneDB ID: retro_mmus_1676

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:91782000..91782441(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 2700062C07Rik
• Ensembl ID: ENSMUSG00000024273
• Aliases: 2700062C07Rik, AI195775, C87515
• Description: RIKEN cDNA 2700062C07 gene [Source:MGI Symbol;Acc:MGI:1915296]

Sequence

>retro_mmus_1676
GAGTACTACCTTACATCAGGCCCTTCAGGCCTAGTGGAAAGCTGCCCAAGTCAGGCTGTTTAGCTCCTCTAGGCCTTTAG
TTCAACAGATAAGGATAACAGCACTTTTCAAGACACATGTCTACACTGCTTTCAATTGTTGCCCTTGGATAACTCAAGAG
TAAATCTCATACCCAAGATCTGCTGATGTCTAAGATACAGAAACTTTTAAATTGAGAAGCAAAAAATCCTACACTCACTT
TTACAAAAAGGGCAACTCTTTAAAAAGTACAAAGCCTCTACAAGTGTATATCTAATTACTTCTAGAACCTGCAAAAGAAC
AGTGGGAAGCAGTGGTGAAAGTAGAAGCTTCTTGTGAGCACTCAAGAGCAACACGGCCACTGGTGTAAACAAAGCCACCC
CAAAGTCAAAAAAGAGAAAGGATCCAGACTCTTCAAGCCTG

Alignment

ORF - retro_mmus_1676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.42 %
• Parental protein coverage: 67.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KYYIEAAARGLVGSCPGQARYLLWAYSSTHEDNSTFQETCPHCFQLLVLDNSRVRLKPKA-KLTPKIQKL
          .YY......GLV.SCP.QA..LL.A.SST..DNSTFQ.TC.HCFQLL.LDNSRV.L.PK...L..KIQKL
Retrocopy EYYLTSGPSGLVESCPSQAV*LL*AFSSTDKDNSTFQDTCLHCFQLLPLDNSRVNLIPKI<LLMSKIQKL

Parental  LNREARNDTLSF-KEAKLLRKYKDSTSVLLITCRTCNRTVRHHGKSRSFLWALKSNAATAANKASPKTPK
          LN.EA.N.TL.F.....L..KYK.STSV.LIT.RTC.RTV...G.SRSFL.ALKSN.AT..NKA.PK..K
Retrocopy LN*EAKNPTLTF>QKGQLFKKYKASTSVYLITSRTCKRTVGSSGESRSFL*ALKSNTATGVNKATPKSKK

Parental  RTAPGSANL
          R..P.S..L
Retrocopy RKDPDSSSL

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	7.78 RPM
SRP007412_cerebellum	0.00 RPM	8.77 RPM
SRP007412_heart	0.00 RPM	2.15 RPM
SRP007412_kidney	0.00 RPM	4.64 RPM
SRP007412_liver	0.00 RPM	3.80 RPM
SRP007412_testis	0.00 RPM	8.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1676 was not detected

EST

No EST(s) were mapped for retro_mmus_1676 retrocopy.

TSS

No TSS is located nearby retro_mmus_1676 retrocopy 5' end.

Lab

retro_mmus_1676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676 , retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,