RetrogeneDB ID: retro_ptro_1976

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:40016050..40016239(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMA7
• Ensembl ID: ENSPTRG00000041769
• Aliases: TMA7, CCDC72
• Description: translation machinery associated 7 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26932]

Sequence

>retro_ptro_1976
ATGTCCAGCCACAAAGGTGGCAAGAAGCCCCTGAAACAGCCCAAGAAGGAGGCCAAGGAGATGGACGAGGAAGAGAAGGC
TTTCAAGCAGAAACAAAAAGAGGAGCAAAAGAAACTCGAGGAGCTAAAAGCGAAGGCTGCGGGGAAGGGGCCCCTGGCCA
CAGGTGAAATTAAGAAATCTGGCAAAAAG

Alignment

ORF - retro_ptro_1976 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGREGGKKKPLKQPKKQAKEMDEEDKAFKQKQKEEQKKLEELKAKAAGKGPLATGGIKKSGKK
          MS...GGKK.PLKQPKK.AKEMDEE.KAFKQKQKEEQKKLEELKAKAAGKGPLATG.IKKSGKK
Retrocopy MSSHKGGKK-PLKQPKKEAKEMDEEEKAFKQKQKEEQKKLEELKAKAAGKGPLATGEIKKSGKK

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	0.00 RPM	72.95 RPM
SRP007412_cerebellum	0.07 RPM	57.07 RPM
SRP007412_heart	0.03 RPM	41.68 RPM
SRP007412_kidney	0.00 RPM	68.39 RPM
SRP007412_liver	0.03 RPM	41.47 RPM
SRP007412_testis	0.11 RPM	78.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1976 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1976 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001193	6 retrocopies	retro_amel_1070, retro_amel_1643, retro_amel_270, retro_amel_503, retro_amel_826, retro_amel_879,
Callithrix jacchus	ENSCJAG00000002871	18 retrocopies	retro_cjac_1370, retro_cjac_1449, retro_cjac_1504, retro_cjac_1667, retro_cjac_1670, retro_cjac_1704, retro_cjac_1918, retro_cjac_2092, retro_cjac_2258, retro_cjac_2422, retro_cjac_2629, retro_cjac_2673, retro_cjac_2692, retro_cjac_2799, retro_cjac_3651, retro_cjac_536, retro_cjac_81, retro_cjac_849,
Felis catus	ENSFCAG00000026902	5 retrocopies	retro_fcat_138, retro_fcat_1630, retro_fcat_173, retro_fcat_57, retro_fcat_630,
Gorilla gorilla	ENSGGOG00000028044	3 retrocopies	retro_ggor_11, retro_ggor_2002, retro_ggor_209,
Mus musculus	ENSMUSG00000091537	11 retrocopies	retro_mmus_1216, retro_mmus_1582, retro_mmus_1632, retro_mmus_2117, retro_mmus_2189, retro_mmus_2222, retro_mmus_2545, retro_mmus_2975, retro_mmus_3235, retro_mmus_389, retro_mmus_412,
Pan troglodytes	ENSPTRG00000041769	9 retrocopies	retro_ptro_136, retro_ptro_1492, retro_ptro_150, retro_ptro_1638, retro_ptro_1953, retro_ptro_1976 , retro_ptro_2312, retro_ptro_2535, retro_ptro_2691,
Rattus norvegicus	ENSRNOG00000042689	2 retrocopies	retro_rnor_316, retro_rnor_894,
Rattus norvegicus	ENSRNOG00000047225	1 retrocopy	retro_rnor_1709,
Sus scrofa	ENSSSCG00000011351	6 retrocopies	retro_sscr_133, retro_sscr_19, retro_sscr_299, retro_sscr_541, retro_sscr_735, retro_sscr_910,