RetrogeneDB ID: retro_ptro_995

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:20407640..20408733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSPTRG00000013795
• Aliases: None
• Description: coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]

Sequence

>retro_ptro_995
ATGGCGCTCCTGCTGCGCTTCGTGCTCCTGTGCGGAGTCGCGGATTTCATCAAAGGTTGGAGTATCACTACTCCTGAGCA
GATAATTGAAAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACGCTTAGTCCTGAAGACCAGGGACCACTGG
ACATCGAGTGGCTGATATCACCAGCTGATAATCAGAAGGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTAT
GATGACTACTATCCAGATCTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
AACGAATTTTCAGCTGTCAGATGTTGGCACAGATCAGTGCAAAGTGAAAAGAGCTCCTGGTGTTGCAAATAGGAAGATTC
AGCTGGTAGTTCTTGGTAAGCCTTCAGGTACAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAATTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACGGAAAATGCCCACTTT
ATGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAATGCTTCTTCTGAGTACTCTGGGACATACAGCTGTACATC
AGAAACAGAGTGGGCTCTGATCAGTGCCTGTTGCGTGTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCAGG
AGCCATTATAGGAACTTTGCTTGCTCTAGCGCTCATTGGTCTTATCATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGAAA
AATATGAAAAGGAAGTTCATCACGATATCAAGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTCCACTGCCAGAAGCTCC
ATAGGCAGTAATCATTCATCCCTGGGATCCATATCTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAAACAAGT
ACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCTAAGTCGAA
TGGGCGCGATTCCTGTGATGATTCCCGCACAGAGCAAGGATGGGTCTATAGTA

Alignment

ORF - retro_ptro_995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLLCFVLLCGVVDFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
          MALLL.FVLLCGV.DF....SITTPE..IEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
Retrocopy MALLLRFVLLCGVADFIKGWSITTPEQIIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV

Parental  IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
          IILYSGDKIYDDYYPDLKGRVHF.SNDLKSGDASINVTN.QLSD.GT.QCKVK.APGVAN.KI.LVVL.K
Retrocopy IILYSGDKIYDDYYPDLKGRVHFKSNDLKSGDASINVTNFQLSDVGTDQCKVKRAPGVANRKIQLVVLGK

Parental  PSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV-KNASSEYSGT
          PSG.RCYVDGSEEIGSDFK.KCEPKEGSLPLQYEWQKLSDS.KMPT.WLAEMTSSVISV.KNASSEYSGT
Retrocopy PSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSRKMPTLWLAEMTSSVISV<KNASSEYSGT

Parental  YSCT-VRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIR
          YSCT..RNRVGSDQCLLR.NVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDI.
Retrocopy YSCT<IRNRVGSDQCLLRVNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIK

Parental  EDVPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSRM
          EDVPPPKSRTSTARS.IGSNHSSLGS.SPSNMEGYSKTQY.QVPSEDFERTPQSPTLPPAKVAAPNLSRM
Retrocopy EDVPPPKSRTSTARSSIGSNHSSLGSISPSNMEGYSKTQYKQVPSEDFERTPQSPTLPPAKVAAPNLSRM

Parental  GAIPVMIPAQSKDGSIV
          GAIPVMIPAQSKDGSIV
Retrocopy GAIPVMIPAQSKDGSIV

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	0.55 RPM	9.54 RPM
SRP007412_cerebellum	0.14 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	14.72 RPM
SRP007412_kidney	0.03 RPM	13.44 RPM
SRP007412_liver	0.03 RPM	19.35 RPM
SRP007412_testis	0.42 RPM	11.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_995 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_995 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1533
Homo sapiens	retro_hsap_1535
Pan troglodytes	retro_ptro_801
Homo sapiens	retro_hsap_1918
Pan troglodytes	retro_ptro_1244
Pan troglodytes	retro_ptro_1444
Pongo abelii	retro_pabe_1273

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012975	1 retrocopy	retro_dnov_990,
Homo sapiens	ENSG00000154639	6 retrocopies	retro_hsap_1533, retro_hsap_1535, retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys	ENSNLEG00000002063	2 retrocopies	retro_nleu_138, retro_nleu_58,
Pongo abelii	ENSPPYG00000011295	2 retrocopies	retro_pabe_1273, retro_pabe_2776,
Pan troglodytes	ENSPTRG00000013795	4 retrocopies	retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995 ,
Sarcophilus harrisii	ENSSHAG00000005309	1 retrocopy	retro_shar_252,