RetrogeneDB ID: retro_ptro_2171

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:98001146..98001746(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC3
• Ensembl ID: ENSPTRG00000014829
• Aliases: None
• Description: None

Sequence

>retro_ptro_2171
ATGGTGCTGGTCCCCACCCACCACTTCAGAGACTTTGAGAGGAAACCAGAGTACCCATAGCTGGAGATGCCTGTCCGACC
TCCCTACCGTGGTCCTATGAGAACCATGTGGCTTATCCACGATGGCTGTGGCATCGCCTGTGCCATCATCACCTGGTTTC
TGGTCCTCTGTGCGGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCCAAGACTATGCATACAGCACCATCAATGGA
ATTGTGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGAGACCGGAGCAGTGCCCAA
ATGAAATGCCACAAATAATTCATCCAGAGTTTACAGATGAAGCCCAGGCATGTGGTATACTCGTGTCCCAGTGCTGCAGC
CTCAAGCCTGACCGAACCTGCCGCTGCAGTGTTTGTAAGGGGTGCATTCGCAGGGTGGACCCCCACTGTCCCTGGGTCAA
CATCTGCATCAAAGAGAACAACCAGAAGTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTGCCTGCCCTCA
TCATGGTGGATTACACTTCCTGGATTGCTGTGAAGAAGAT

Alignment

ORF - retro_ptro_2171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.04 %
• Parental protein coverage: 61.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMLIPTHHFRNIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
          M.L.PTHHFR..ERKPEY...E..V.PPY.GP..TMW.I.DGCGIACAI.TWFLVL.AEFVVLF.MLIPS
Retrocopy MVLVPTHHFRDFERKPEYP*LEMPVRPPYRGPMRTMWLIHDGCGIACAIITWFLVLCAEFVVLFFMLIPS

Parental  RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNAT-KEFIESLQLKPGQVVYKCP-KCCSIKPD
          .DY.YS.INGIVFNLL.FLALASHC.AMLT..GAVPK.NAT.K.FI.SLQ.KP..VVY.CP..CCS.KPD
Retrocopy QDYAYSTINGIVFNLLTFLALASHCQAMLTETGAVPK*NAT<K*FIQSLQMKPRHVVYSCP<QCCSLKPD

Parental  RAHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEED
          R...CSVCK.CIR..D.HCPWVN.C..ENNQK.FVLF.M..ALISL.ALIMV.G.HFL.C.EED
Retrocopy RTCRCSVCKGCIRRVDPHCPWVNICIKENNQKCFVLFIMCTALISLPALIMV<GLHFLDCCEED

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	0.00 RPM	30.44 RPM
SRP007412_cerebellum	0.00 RPM	53.52 RPM
SRP007412_heart	0.00 RPM	37.92 RPM
SRP007412_kidney	0.03 RPM	65.14 RPM
SRP007412_liver	0.00 RPM	44.78 RPM
SRP007412_testis	0.11 RPM	108.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2171 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2171 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3221
Gorilla gorilla	retro_ggor_2187
Pongo abelii	retro_pabe_2668

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163812	1 retrocopy	retro_hsap_3221,
Pongo abelii	ENSPPYG00000013950	1 retrocopy	retro_pabe_2668,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Pan troglodytes	ENSPTRG00000014829	1 retrocopy	retro_ptro_2171 ,