RetrogeneDB ID: retro_ptro_2804

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:6348096..6348534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000039581
• Aliases: None
• Description: None

Sequence

>retro_ptro_2804
GGTTATAGGCGGGTGTTTGAGGAGTACATGTGGGTTATTAGCCAGGGGTACCCAGACATCCGTATTGAAGGAGAGAATTA
CCTCCCTCAACCAATGTATAGACACATAGCATCTTTCCTGTCAGTCTTCAAACTAGTATTAATAAGCTTAATAATTGTTG
GCAAGGATCCTTTTGCTTTCTTTGGCATGCAAGCTCCTAGCATCTGGCAGTGGGGCCAAGAAAATAAGGTCTATGCAAGT
ATGATGGTTTTCTTCTTGAGCAACATGATTGAGAACCAGTGTATGTCAACAGGTGCATTTGAGATAACTTTAAATGATGT
ACCTGTGTGGTCTAAGCTGGAATCCGGTCACCTTCCATCCATGCAACAACTTGTTCAAATTCTTGACAATGAAATGAAGC
TCAATGTGCATATGGATTCAATCCCACACCATCGATCG

Alignment

ORF - retro_ptro_2804 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.58 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQ
          GYRRVFEEYM.VISQ.YPDIRIEGENYLPQP.YRHIASFLSVFKLVLI.LIIVGKDPFAFFGMQAPSIWQ
Retrocopy GYRRVFEEYMWVISQGYPDIRIEGENYLPQPMYRHIASFLSVFKLVLISLIIVGKDPFAFFGMQAPSIWQ

Parental  WGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDS
          WGQENKVYA.MMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDS
Retrocopy WGQENKVYASMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDS

Parental  IPHHRS
          IPHHRS
Retrocopy IPHHRS

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	1.45 RPM	17.82 RPM
SRP007412_cerebellum	1.94 RPM	14.09 RPM
SRP007412_heart	0.64 RPM	9.15 RPM
SRP007412_kidney	2.88 RPM	25.39 RPM
SRP007412_liver	1.11 RPM	7.95 RPM
SRP007412_testis	0.21 RPM	9.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2804 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2804 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4126
Pongo abelii	retro_pabe_3478

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804 ,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,