RetrogeneDB ID: retro_ptro_801

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:18091050..18092144(+)
• 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_801
ATAGCACTCCTGCTGCGCTTCGTGCTCCTGTGCGGAGTCGCGGATTTCATCAGAGGTTGGAGTATCACTACTCCTGAGCA
GATGATTGAAAAAGCCAAAGGGGAAACTGGCCTATCTGCCATGCAAATTTATGCTTAGTCCTGAAGACCAGGGACCACTG
GACATCGAGTGGCTGGTATCACCAGCTGATAATCAGAAGGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTA
TGATGACTACTATCCAGATCTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATG
TAACGAATTTTCAGCTGTCAGATATTGGCACAGATCAGTGCAAAGTGAAAAGAGCTCCTGGTGTTGCAAATAGGAAGATT
CAGCTGGTAGTTCTTGGTAAGCCTTCAGGTACAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAATT
AAAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTT
TATGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAATGCTTCTTCTGAGTACTCTGGGACATACAGCTGTAAAT
CAGAAACAGAGTGGGCTCTGATCAGTGCCTGTTGCGTGTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCAG
GAGCCATTATAGGAACTTTGCTTGCTCTAGCGCTCATTGGTCTTATCATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGAA
AAATATGAAAAGGAAGTTCATCACGATATCAAGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTCCACTGCCAGAAGCTA
CATAGGCAGTAATCATTCATCCCTGGGATCCATATCTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAAACAAG
TACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCTAAGTCGA
ATGGGCGCGATTCCTGTGATGATTCCCGCACAGAGCAAGGATGGGTCTATAGTA

Alignment

ORF - retro_ptro_801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALLLCFVLLCGVVDFARSLSITTPEEMIEKAKGET-AYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQ
          .ALLL.FVLLCGV.DF.R..SITTPE.MIEKAKGET.AYLPCKF.LSPEDQGPLDIEWL.SPADNQKVDQ
Retrocopy IALLLRFVLLCGVADFIRGWSITTPEQMIEKAKGET>AYLPCKFMLSPEDQGPLDIEWLVSPADNQKVDQ

Parental  VIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLV
          VIILYSGDKIYDDYYPDLKGRVHF.SNDLKSGDASINVTN.QLSDIGT.QCKVK.APGVAN.KI.LVVL.
Retrocopy VIILYSGDKIYDDYYPDLKGRVHFKSNDLKSGDASINVTNFQLSDIGTDQCKVKRAPGVANRKIQLVVLG

Parental  KPSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV-KNASSEYSG
          KPSG.RCYVDGSEEIGSDFK.KCEPKEGSLPLQYEWQKLSDSQKMPT.WLAEMTSSVISV.KNASSEYSG
Retrocopy KPSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTLWLAEMTSSVISV<KNASSEYSG

Parental  TYSCT-VRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDI
          TYSC...RNRVGSDQCLLR.NVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDI
Retrocopy TYSCK<IRNRVGSDQCLLRVNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDI

Parental  REDVPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSR
          .EDVPPPKSRTSTARSYIGSNHSSLGS.SPSNMEGYSKTQY.QVPSEDFERTPQSPTLPPAKVAAPNLSR
Retrocopy KEDVPPPKSRTSTARSYIGSNHSSLGSISPSNMEGYSKTQYKQVPSEDFERTPQSPTLPPAKVAAPNLSR

Parental  MGAIPVMIPAQSKDGSIV
          MGAIPVMIPAQSKDGSIV
Retrocopy MGAIPVMIPAQSKDGSIV

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	9.54 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	14.72 RPM
SRP007412_kidney	0.00 RPM	13.44 RPM
SRP007412_liver	0.00 RPM	19.35 RPM
SRP007412_testis	5.16 RPM	11.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_801 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_801 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1533
Homo sapiens	retro_hsap_1535
Pan troglodytes	retro_ptro_995
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,