RetrogeneDB ID: retro_mmus_2257

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:58761864..58762230(-)
• Located in intron of: ENSMUSG00000097725

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cisd2
• Ensembl ID: ENSMUSG00000028165
• Aliases: Cisd2, 1500009M05Rik, 1500026J14Rik, 1500031D15Rik, AI848398, B630006A20Rik, Miner1, Noxp70, Zcd2
• Description: CDGSH iron sulfur domain 2 [Source:MGI Symbol;Acc:MGI:1914256]

Sequence

>retro_mmus_2257
ATGGTGGAAGTGGAGCTGCCCACCCACCTCAAGCAGCCCCCACTCCCGAGAGCATTACCAGCTGCGCCCCACCGCAATTT
CAGAATGGCTCCACTTACTGCCCTTCCGTGGGGTGCTTGCTTGTCTTGGCTACCGTGTTGCCACTTGTCCATTCTTCCCA
AAGAAGAAATAACAGAATAGCTTGATTAATCTTAAAATACAAAAAGAAAATCCCAAGGTGGTGAATATAATAAATGTTGA
AGATCTCAGTCTTACTAAAGGAGCTGATTGTAGGTGCTAGTGTTCCAAGACCTTCCCTGCCTGTGATGATCTTATCATAA
ACACAATGAACATACCATGGGTCCTCTCATCCCGAAGAAGACAGAA

Alignment

ORF - retro_mmus_2257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IVKVQLPAYLKQ-LPVPDSITGFAR-LTVSDWLRLLPFLGVLALLGY-LAVRPFFPKKKQQKDSLINLKI
          .V.V.LP..LKQ..P.P.SIT..A.....S.WL.LLPF.GVLA.LGY..A..PFFPKKK.Q..SLINLKI
Retrocopy MVEVELPTHLKQ<APTPESITSCAP<TAISEWLHLLPFRGVLACLGYRVATCPFFPKKK*Q-NSLINLKI

Parental  QKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDG-SHNKHNELTGDNVGPLILKKKE
          QKENPKVVN.IN.EDL.LTK.A.CRC..SKTFPACD..S..KHNE.T....GPLI.KK.E
Retrocopy QKENPKVVNIINVEDLSLTKGADCRC*CSKTFPACDD<SYHKHNEHT---MGPLIPKKTE

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	0.02 RPM	42.80 RPM
SRP007412_cerebellum	0.00 RPM	42.03 RPM
SRP007412_heart	0.03 RPM	76.70 RPM
SRP007412_kidney	0.00 RPM	76.69 RPM
SRP007412_liver	0.00 RPM	38.75 RPM
SRP007412_testis	0.09 RPM	8.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2257 was not detected

EST

No EST(s) were mapped for retro_mmus_2257 retrocopy.

TSS

No TSS is located nearby retro_mmus_2257 retrocopy 5' end.

Lab

retro_mmus_2257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010779	1 retrocopy	retro_cfam_1012,
Callithrix jacchus	ENSCJAG00000015530	1 retrocopy	retro_cjac_2668,
Felis catus	ENSFCAG00000028054	1 retrocopy	retro_fcat_1979,
Mus musculus	ENSMUSG00000028165	1 retrocopy	retro_mmus_2257 ,
Nomascus leucogenys	ENSNLEG00000026930	1 retrocopy	retro_nleu_1331,
Oryctolagus cuniculus	ENSOCUG00000013943	1 retrocopy	retro_ocun_1444,
Ictidomys tridecemlineatus	ENSSTOG00000001408	1 retrocopy	retro_itri_869,