RetrogeneDB ID: retro_mmus_2651

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:49900287..49901293(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ckap2
• Ensembl ID: ENSMUSG00000037725
• Aliases: Ckap2, AI461656, AW228814, LB1
• Description: cytoskeleton associated protein 2 [Source:MGI Symbol;Acc:MGI:1931797]

Sequence

>retro_mmus_2651
AAAGATACTGACCAGAGCAGATACACGATCGCAGGAGCAATGGTTCATAGATCAGCTCAGCTCAAAGACACCGCAGCAGA
GAGGAAAGCTCAGATGGCCAAGTGGAGAACTGGCAATGGAAAGGGGCTAAAATGACCTCCTCAGTCACTAGTCACCCAGG
CTGAGCCAAAGGGGTAAAATGAAAACCCAGCTGGATCCTTTTGGACTACCATGGCAGAAGAAGATGAACAGAGATTATTT
ACTGAAAAAGTAAACAAAACTATTTCTGAATGCCTGAACCTCATTAGTAAGGGGTGCCCAAAAGAAGAAATTTTAGCTAC
ATTGAATGACCTAATTCATAATATCCCAGATGCCAAAAAAACTTGTTAAATATTGGATATGTCTTGTATGTATTGAACCA
ATCACAAGTCCTATTGAAAATATTATCTAAATCTACAAGAAGGCCATTCTGGCAGGGGCTCAGCCTATTGAAGAGATTCA
ACATATAATAATAGATATTCTAACAACAAAGAATCATGAAAAAGTCATTTTGGGAGAAAATATTGAGGAGGCTCATGCAA
CCAAGGAACATATCCAAGAAGTAAATGTGCAAGCTAATCTAGGGTCAGGAAAACCAGAAGAGGAGAATGAACATCATGGA
AAAGTTGAGGTTTATGAAGACGATCAAGACAACACAAGGAAAGATCCAACCAAAGATTTAACAACCCCAAACTCAAAAAC
TGAAGCAGGTTGCATAATTCGATATAATGTATCTTCTATACCAAAGAATGAAAAGATGCAACATGATAAAAATTCCACAT
TTAATAGAGCTAAAGTTCCTGACACCAGTGAGACATTCATGACGCATTCAAGACAAGACTTTCAAACTGCCAGCCTTGTT
AAAAGACCATGGCCCTTCTGTGTCTTCCCTGGAACAGTTGTCTGAGTTGGGAGGGCATGCTTTGCTTGCCACCCTAATGC
TGCACTGTGCCCTCTGTTCATTGAAAGCGACGTAGCAGAAGAGGAA

Alignment

ORF - retro_mmus_2651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.16 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KDTDQRRYTIAGASVHRSAQLKDTTAERKAQMTEWRTGKGKGLKRPPHSVVTQAEPKGQSENPVGSFWTT
          KDTDQ.RYTIAGA.VHRSAQLKDT.AERKAQM..WRTG.GKGLK.PP.S.VTQAEPKG..ENP.GSFWTT
Retrocopy KDTDQSRYTIAGAMVHRSAQLKDTAAERKAQMAKWRTGNGKGLK*PPQSLVTQAEPKG*NENPAGSFWTT

Parental  MAEEDEQRLFTEKVNKTISECLNLINEGCPKEEILATLNDLIHNIPDA-KKLVKYWICLVRIEPITSPIE
          MAEEDEQRLFTEKVNKTISECLNLI..GCPKEEILATLNDLIHNIPDA.KKLVKYWICLV.IEPITSPIE
Retrocopy MAEEDEQRLFTEKVNKTISECLNLISKGCPKEEILATLNDLIHNIPDA>KKLVKYWICLVCIEPITSPIE

Parental  NIISIYEKAILAGAQPIEEMRHIIIDILTTKSQEKVNLGENIEEAHATKEPIQEVNADANVGSGKPGEEN
          NII.IY.KAILAGAQPIEE..HIIIDILTTK..EKV.LGENIEEAHATKE.IQEVN..AN.GSGKP.EEN
Retrocopy NII*IYKKAILAGAQPIEEIQHIIIDILTTKNHEKVILGENIEEAHATKEHIQEVNVQANLGSGKPEEEN

Parental  EHHGKVEVYEDDQDNKIKDP--DLTTPDSKTEAGCIIRYNVSSTPRLQSMKKMQHDKNST-LKELKFLTP
          EHHGKVEVYEDDQDN..KDP..DLTTP.SKTEAGCIIRYNVSS.P......KMQHDKNST.L.ELKFLTP
Retrocopy EHHGKVEVYEDDQDNTRKDPTKDLTTPNSKTEAGCIIRYNVSSIPK---NEKMQHDKNST>LIELKFLTP

Parental  VRRSRRIQDKTSRLPAMLKDHDPSVSSLEQLSELGGDA-FVCRPNAALCPLFFETDVAEEE
          VR.S.RIQDKT..LPA.LKDH.PSVSSLEQLSELGG.A.F.C.PNAALCPLF.E.DVAEEE
Retrocopy VRHS*RIQDKTFKLPALLKDHGPSVSSLEQLSELGGHA<FACHPNAALCPLFIESDVAEEE

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	0.26 RPM
SRP007412_cerebellum	0.00 RPM	0.30 RPM
SRP007412_heart	0.00 RPM	0.37 RPM
SRP007412_kidney	0.00 RPM	0.77 RPM
SRP007412_liver	0.03 RPM	0.05 RPM
SRP007412_testis	0.00 RPM	12.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2651 was not detected

EST

No EST(s) were mapped for retro_mmus_2651 retrocopy.

TSS

No TSS is located nearby retro_mmus_2651 retrocopy 5' end.

Lab

retro_mmus_2651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2651 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651 ,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,