RetrogeneDB ID: retro_ptro_2556

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:106792216..106792781(+)
• Located in intron of: ENSPTRG00000019564

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD4
• Ensembl ID: ENSPTRG00000016632
• Aliases: RWDD4, RWDD4A
• Description: None

Sequence

>retro_ptro_2556
ATGAGTGCCAACGAGGACCAGGAGATGGAACTAGAAGCATTACGCTCTATTTATGAAGGAGATGAAAGTTTCCGGGAATT
AAGTTCAGTTTCTTTTCAATATAGGATAGGTGAAAATGGTGATCCCAAAGCCTTCTTAATAGAGATTTCCTGGACAGAAA
CATATCCCCAAACACCTCCAATTCTATCTATGAATGCTTTTTTTTAACAACACCGTATCATCAGCTGTAAAGCAGAGTAT
ATTAGCCAAGTTACAGGAAGCAGTAGAAGCTAATCTTGGAACCGCTATGACCTGTACATTGTTTGAATATGCCAAAGACA
ATAAAGAGCAGTTCATGGAGAATCACAATCCCATTAATTCCACAACATCGATAAGCAATATCATCTCAATTGAAACTCCT
AATACAGCCCCATCAAGTAAGAAAAAAGACAAAAAAGAATAACTTTCAAAAGCCCAGAAGCGTAAGCTGGCAGACAAAAC
AGATCACAAAGGAGAACTTCCTCGAGGCTGGAATTGGGTTGATGTTGTGAAGCATTTAAGCAAAACTGGCTCTAAGGATG
ATGAG

Alignment

ORF - retro_ptro_2556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSANEDQEMELEALRSIYEGDESFRELSPVSFQYRIGENGDPKAFLIEISWTETYPQTPPILSMNAFF-N
          MSANEDQEMELEALRSIYEGDESFRELS.VSFQYRIGENGDPKAFLIEISWTETYPQTPPILSMN....N
Retrocopy MSANEDQEMELEALRSIYEGDESFRELSSVSFQYRIGENGDPKAFLIEISWTETYPQTPPILSMNXXX>N

Parental  NTISSAVKQSILAKLQEAVEANLGTAMTYTLFEYAKDNKEQFMENHNPINSATSISNIISIETPNTAPSS
          NT.SSAVKQSILAKLQEAVEANLGTAMT.TLFEYAKDNKEQFMENHNPINS.TSISNIISIETPNTAPSS
Retrocopy NTVSSAVKQSILAKLQEAVEANLGTAMTCTLFEYAKDNKEQFMENHNPINSTTSISNIISIETPNTAPSS

Parental  KKKDKKEQLSKAQKRKLADKTDHKGELPRGWNWVDVVKHLSKTGSKDDE
          KKKDKKE.LSKAQKRKLADKTDHKGELPRGWNWVDVVKHLSKTGSKDDE
Retrocopy KKKDKKE*LSKAQKRKLADKTDHKGELPRGWNWVDVVKHLSKTGSKDDE

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	0.07 RPM	4.79 RPM
SRP007412_cerebellum	0.07 RPM	3.30 RPM
SRP007412_heart	0.03 RPM	6.97 RPM
SRP007412_kidney	0.00 RPM	9.10 RPM
SRP007412_liver	0.00 RPM	3.80 RPM
SRP007412_testis	0.11 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2556 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2556 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3770
Gorilla gorilla	retro_ggor_2536

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003081	1 retrocopy	retro_btau_603,
Canis familiaris	ENSCAFG00000007880	1 retrocopy	retro_cfam_1281,
Choloepus hoffmanni	ENSCHOG00000005290	3 retrocopies	retro_chof_1477, retro_chof_441, retro_chof_887,
Dasypus novemcinctus	ENSDNOG00000015132	1 retrocopy	retro_dnov_968,
Felis catus	ENSFCAG00000024337	1 retrocopy	retro_fcat_1156,
Homo sapiens	ENSG00000182552	2 retrocopies	retro_hsap_3770, retro_hsap_3841,
Gorilla gorilla	ENSGGOG00000011982	1 retrocopy	retro_ggor_2536,
Myotis lucifugus	ENSMLUG00000006800	1 retrocopy	retro_mluc_545,
Monodelphis domestica	ENSMODG00000004223	2 retrocopies	retro_mdom_1015, retro_mdom_251,
Nomascus leucogenys	ENSNLEG00000010733	1 retrocopy	retro_nleu_1898,
Otolemur garnettii	ENSOGAG00000016709	5 retrocopies	retro_ogar_1084, retro_ogar_1171, retro_ogar_1228, retro_ogar_2652, retro_ogar_2789,
Ochotona princeps	ENSOPRG00000015147	1 retrocopy	retro_opri_1002,
Pongo abelii	ENSPPYG00000015230	1 retrocopy	retro_pabe_3082,
Pan troglodytes	ENSPTRG00000016632	2 retrocopies	retro_ptro_1456, retro_ptro_2556 ,
Rattus norvegicus	ENSRNOG00000022500	1 retrocopy	retro_rnor_2930,
Sarcophilus harrisii	ENSSHAG00000011971	1 retrocopy	retro_shar_760,
Sus scrofa	ENSSSCG00000015776	2 retrocopies	retro_sscr_1019, retro_sscr_1051,
Ictidomys tridecemlineatus	ENSSTOG00000013086	1 retrocopy	retro_itri_533,
Tarsius syrichta	ENSTSYG00000006599	1 retrocopy	retro_tsyr_1898,
Vicugna pacos	ENSVPAG00000005743	1 retrocopy	retro_vpac_341,