RetrogeneDB ID: retro_ptro_700

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:70452515..70453456(+)
• Located in intron of: ENSPTRG00000005221

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAHD2A
• Ensembl ID: ENSPTRG00000012214
• Aliases: FAHD2A, FAHD2B
• Description: None

Sequence

>retro_ptro_700
ATGCTGGTCTCTGGTAGAAGAAGGTTGCTCACAGCTCTGCTGCAGGCTCAGAAGTGGCCCTTTCAACCCTCCAGAGACAT
GAGACTAGTCCAGTTCCAGGCACCCCACCTGGTGGGGCCTCACTTGGGCCCAGAGATGGGGAATGGTGGAAGGGTTATCA
ACCTCAGTGCCTTTGACTCTATGCTCCCCAAAATGATGACACAGTTCCTAGAGCAGGGAGAGGCCATCCTCTCAGTGGCA
AGAAGAGCCTTGGGTGCCCAGTTGCCAGTCCTACCATGGTTGGAAGTAACCTCCCTGGCTCCAGCCACATGGCCAGATAA
GGTGGTGTGTGTGGGCATGAATTATGTGGACCACTGCAAAGAACAGAATGTGCCCATGCCCATGGAACACATCAACTTCA
GCAAGTTTGCCAACTCCATTATGGAGCCCTATGATGAGATGGTTCTCCCATCAGAGAGCCAGGAGGTAGACTGGGAAGTG
GAGCAGCTGTGGTCATTGGAAAGAAAGGCAAGCACATCAAGGCCACAGATGCCATGGCCCATATGGCTGGCTTCACTGCG
GCTCATAACGTGAGTGCTCGTGACTGGCAAATGAGACATGATGGGAAACAGTGGCTGCTGGGAAAAACCTTCGACACCTT
CTGCCCTCTGGGCCTTGCCTTGGTGACCAAGGACAGTGTAGCAGATGCACACATCTTAAACATCTGCTGCCAAGTGAATG
GGGAAGTGGTCCAGAGCAACAACACCAACCAGATGGTGGTCAAGACAGAGGAGCGGATAGCCTGGGTCTCCCAGTTTGTC
ACCTTTTACCCAGGGGATGTCATCCTGACTGGGACCTCCCCAGGTGTTGGTGTATTCAGGAAACCTCCTGTCTTTCTCAA
GAAGGGAGATGAAGTCCAGTATGAAATTGAAGAACTAGGTGTCATCATCAGCAAGGTGGTG

Alignment

ORF - retro_ptro_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVSGRRRLLTVLLQAQKWPFQPSRDMRLVQFRAPHLVGPHLGLETGNGGGVINLSAFDPTLPKTMTQFL
          MLVSGRRRLLT.LLQAQKWPFQPSRDMRLVQF.APHLVGPHLG.E.GNGG.VINLSAFD..LPK.MTQFL
Retrocopy MLVSGRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVGPHLGPEMGNGGRVINLSAFDSMLPKMMTQFL

Parental  EQGEATLSVARRALAAQLPVLPRSEVTFLAPVTRPDKVVCVGMNYVDHCKEQNVPVPKEPIIFSKFASSI
          EQGEA.LSVARRAL.AQLPVLP..EVT.LAP.T.PDKVVCVGMNYVDHCKEQNVP.P.E.I.FSKFA.SI
Retrocopy EQGEAILSVARRALGAQLPVLPWLEVTSLAPATWPDKVVCVGMNYVDHCKEQNVPMPMEHINFSKFANSI

Parental  VGPYDEVVLPPQSQEVDWEVE-LAVVIGKKGKHIKATDAMAHVAGFTVAHDVSARDWQMRRNGKQWLLGK
          ..PYDE.VLP..SQEVDWEVE..AVVIGKKGKHIKATDAMAH.AGFT.AH.VSARDWQMR..GKQWLLGK
Retrocopy MEPYDEMVLPSESQEVDWEVE<AAVVIGKKGKHIKATDAMAHMAGFTAAHNVSARDWQMRHDGKQWLLGK

Parental  TFDTFCPLGPALVTKDSVADPHNLKICCRVNGEVVQSSNTNQMVFKIEDLIAWVSQFVTFYPGDVILTGT
          TFDTFCPLG.ALVTKDSVAD.H.L.ICC.VNGEVVQS.NTNQMV.K.E..IAWVSQFVTFYPGDVILTGT
Retrocopy TFDTFCPLGLALVTKDSVADAHILNICCQVNGEVVQSNNTNQMVVKTEERIAWVSQFVTFYPGDVILTGT

Parental  PPGVGVFRKPPVFLKKGDEVQCEIEELGVIINKVV
          .PGVGVFRKPPVFLKKGDEVQ.EIEELGVII.KVV
Retrocopy SPGVGVFRKPPVFLKKGDEVQYEIEELGVIISKVV

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	0.04 RPM	15.16 RPM
SRP007412_cerebellum	0.50 RPM	10.93 RPM
SRP007412_heart	0.09 RPM	8.95 RPM
SRP007412_kidney	0.03 RPM	15.04 RPM
SRP007412_liver	0.03 RPM	18.30 RPM
SRP007412_testis	0.00 RPM	22.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_700 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_700 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1025
Gorilla gorilla	retro_ggor_810
Pongo abelii	retro_pabe_860
Macaca mulatta	retro_mmul_818

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018863	1 retrocopy	retro_cjac_3222,
Gorilla gorilla	ENSGGOG00000016246	1 retrocopy	retro_ggor_810,
Macaca mulatta	ENSMMUG00000012859	1 retrocopy	retro_mmul_818,
Nomascus leucogenys	ENSNLEG00000000008	1 retrocopy	retro_nleu_903,
Pongo abelii	ENSPPYG00000012057	1 retrocopy	retro_pabe_860,
Pan troglodytes	ENSPTRG00000012214	1 retrocopy	retro_ptro_700 ,