RetrogeneDB ID: retro_ptro_1598

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:54856146..54856685(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSPTRG00000000865
• Aliases: None
• Description: None

Sequence

>retro_ptro_1598
GAGGGTGTTCTGGTTCATGGGGCGAGTGGAGAAGTTGGATTAGCAGCATGCCAAATTGCTAGAGCTTATGGCTTAAAGGT
TTTGGGCACTGCTGGTACTGAGGAAGGACAAAAGGTTGTTTTGCAAAATGGAGTCCATTAAGTCTTCAGTCACAGAGAAG
TTAATTATATTGACAAAATTAAGAAATATGTTGGTGAGAAAGGAATTGACATAATTATTGAAATGTTAGCTAATGTAAAT
CTTAGTAAAGATTTGAGTCTTCTGTCACATAGAGGATGAGTGATAGTTGTTGGCAACAGAGGTACTATGGAAATAAACCC
ACGGGACACCATGGCAAAGGAGTTGGGTATAATTGGAGTTACTCTCTTTTCCTCAACCAAGGAGGAATTTCAGTAATATG
CAGCCACCCTTCAAGCTGGAAAGGAAGTTGGTTGGTTGAAACCTGTAACAGGTTCTCAATATCCACTGGAGAAGGTGGCC
CAGGCTCATGAAAATATCATTCATGGCAGTGGGGCTACTGGAAAATGATTATTCTCTTA

Alignment

ORF - retro_ptro_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 54.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESVLVHGASGGVGLAACQIARAYGLKVLGTAGTEEGQKIVLQNGAHEVFNHREVNYIDKIKKYVGEKGID
          E.VLVHGASG.VGLAACQIARAYGLKVLGTAGTEEGQK.VLQNG.H.VF.HREVNYIDKIKKYVGEKGID
Retrocopy EGVLVHGASGEVGLAACQIARAYGLKVLGTAGTEEGQKVVLQNGVH*VFSHREVNYIDKIKKYVGEKGID

Parental  VIIEMLANVNLSKDLSLLSHGGRVIVVGSRGTIEINPRDTMAKESSIIGVTLFSSTKEEFQQYAAALQAG
          .IIEMLANVNLSKDLSLLSH.G.VIVVG.RGT.EINPRDTMAKE..IIGVTLFSSTKEEFQ.YAA.LQAG
Retrocopy IIIEMLANVNLSKDLSLLSHRG*VIVVGNRGTMEINPRDTMAKELGIIGVTLFSSTKEEFQ*YAATLQAG

Parental  MEIGWLKPVIGSQYPLEKVAEAHENIIHGSGATG-KMILLL
          .E.GWLKPV.GSQYPLEKVA.AHENIIHGSGATG.KMI.LL
Retrocopy KEVGWLKPVTGSQYPLEKVAQAHENIIHGSGATG<KMIILL

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_prefrontal_cortex	0.02 RPM	19.00 RPM
SRP007412_cerebellum	0.00 RPM	15.24 RPM
SRP007412_heart	0.09 RPM	67.12 RPM
SRP007412_kidney	0.03 RPM	167.24 RPM
SRP007412_liver	0.00 RPM	96.50 RPM
SRP007412_testis	0.00 RPM	11.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1598 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1598 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,