RetrogeneDB ID: retro_mmus_1314

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:118375345..118375951(-)
• Located in intron of: ENSMUSG00000096997

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cryz
• Ensembl ID: ENSMUSG00000028199
• Aliases: Cryz, Sez9
• Description: crystallin, zeta [Source:MGI Symbol;Acc:MGI:88527]

Sequence

>retro_mmus_1314
GTCTCTGGTGGCTAGGCAGACTTTGCTCTCGCAGCAGATCACATTATCTACCTGCTGCCAGAGATGCTGGGCTTCAGGCA
GGAGGCTGCCCTGGGGATCCCGTACTTCATGGCCTGGCGAGCTTTGTTCCGTAGTGCAGGTGCGCGAGCTGGGGAAAGCT
TGCAGGTTCTCGGGGCCAGCGGAGGAGTTGGATTAGCTTCATGCCAGATTGCCTGAGCTCATGGCTTAAAGGTTTTGGGC
ACAGCTGGTTCTGAGGAAGGAATAAAGCTTCATCATGAAGCTTTTAATAGAGTCCACGAAGTGTTTAATCCCAAAGAAGC
CAACTATCTTGATAAAATCAAGACGTCTGTTGGTACAAGGGTTGATGTGATGGCTGAGATGCTGGCGAATGAGAACCTTA
GCAATGACCTGAAGCTTCTATGGTAGAGAGGACGGGTCACTGTTGTTGGCTGTAGAGGTCTCATTGAGATAATCCCAAGG
ATCACCTTGGCAAAAGAGACAAGTATAATTGGAGTCTCTCTCTTTTCAAGCACAGAGGAGGACTTTCAGCCATTCGCAGG
CACCCTCCAAGCAGGAATGGAAAAAGGTCAGGTGACGCCTGTTCTG

Alignment

ORF - retro_mmus_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.63 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSGGYAEFALAADDTIYPLPETLNFRQGAALGIPYFTACRALFHSARARAGESVLVHGASGGVGLATCQI
          VSGG.A.FALAAD..IY.LPE.L.FRQ.AALGIPYF.A.RALF.SA.ARAGES..V.GASGGVGLA.CQI
Retrocopy VSGG*ADFALAADHIIYLLPEMLGFRQEAALGIPYFMAWRALFRSAGARAGESLQVLGASGGVGLASCQI

Parental  ARAHGLKVLGTAGSEEGKKLVLQ--NGAHEVFNHKEANYIDKIKMSVGDKDKGVDVIIEMLANENLSNDL
          A.AHGLKVLGTAGSEEG.KL.....N..HEVFN.KEANY.DKIK.SVG.....VDV..EMLANENLSNDL
Retrocopy A*AHGLKVLGTAGSEEGIKLHHEAFNRVHEVFNPKEANYLDKIKTSVGTR---VDVMAEMLANENLSNDL

Parental  KLLSHGGRVVVVGCRGPIEINPRDTMAKETSIIGVSLSSSTKEEFQQFAGLLQAGIEKGWVKPVI
          KLL...GRV.VVGCRG.IEI.PR.T.AKETSIIGVSL.SST.E.FQ.FAG.LQAG.EKG.V.PV.
Retrocopy KLLW*RGRVTVVGCRGLIEIIPRITLAKETSIIGVSLFSSTEEDFQPFAGTLQAGMEKGQVTPVL

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	11.47 RPM
SRP007412_cerebellum	0.00 RPM	11.42 RPM
SRP007412_heart	0.00 RPM	7.60 RPM
SRP007412_kidney	0.00 RPM	214.11 RPM
SRP007412_liver	0.00 RPM	64.83 RPM
SRP007412_testis	0.78 RPM	5.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1314 was not detected

EST

No EST(s) were mapped for retro_mmus_1314 retrocopy.

TSS

No TSS is located nearby retro_mmus_1314 retrocopy 5' end.

Lab

retro_mmus_1314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314 ,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,