RetrogeneDB ID: retro_ptro_1694

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:132027919..132028470(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038646
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNA14
• Ensembl ID: ENSPTRG00000021042
• Aliases: None
• Description: None

Sequence

>retro_ptro_1694
ACGCAACAAGATGTGCTTAGAGTTCGAGTCCCCACCACAGGGATCGTCGAATACCCCTTTGACTTACAAAGTGTCATTTT
CAGAATGTTCGATGTAGGGGGCCAAAGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGT
TTCTAGTAGCGCTTAGTGAATATGATCAAGTTCTCGTGGAGTCAGACAATGAGAACCGAATGGAGGAAAGCAAGGCTCTC
TTTAGTACAATTATCACGTATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTGTTAAACAAGAAAGATCTTCCAGAGGA
GAAAATCACGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCCCGAGAAT
TCATTCTGAAGATGTTCGTGGACCTGAACCCAGTGACGAAATTATCTACTCCCACTTCACATGCGCCACAGACACCGAGA
ATATCCGCTTTGTGTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGATTACAATCTGGTC

Alignment

ORF - retro_ptro_1694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.18 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TQQDVLRVRVPTTGIIEYPFDLENIIFRMVDVGGQRSERRKWIHCFESVTSIIFLVALSEYDQVLAECDN
          TQQDVLRVRVPTTGI.EYPFDL...IFRM.DVGGQRSERRKWIHCFE.VTSI.FLVALSEYDQVL.E.DN
Retrocopy TQQDVLRVRVPTTGIVEYPFDLQSVIFRMFDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDN

Parental  ENRMEESKALFKTIITYPWFLNSSVILFLNKKDLLEEKIMYSHLISYFPEYTGPKQDVKAARDFILKLYQ
          ENRMEESKALF.TIITYPWF.NSSVIL.LNKKDL.EEKI.YSHL..YFPEY.GP..D..AAR.FILK...
Retrocopy ENRMEESKALFSTIITYPWFQNSSVILLLNKKDLPEEKITYSHLVDYFPEYDGPQRDAQAAREFILKMFV

Parental  DQN-PDKEKVIYSHFTCATDTDNIRFVFAAVKDTILQLNLREFNLV
          D.N.P..E..IYSHFTCATDT.NIRFVFAAVKDTILQLNL...NLV
Retrocopy DLN<PSDE-IIYSHFTCATDTENIRFVFAAVKDTILQLNLKDYNLV

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	0.09 RPM	0.88 RPM
SRP007412_cerebellum	0.04 RPM	2.72 RPM
SRP007412_heart	0.03 RPM	2.10 RPM
SRP007412_kidney	0.00 RPM	3.48 RPM
SRP007412_liver	0.00 RPM	3.90 RPM
SRP007412_testis	7.27 RPM	15.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1694 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013561	1 retrocopy	retro_ggor_2605,
Pan troglodytes	ENSPTRG00000021042	1 retrocopy	retro_ptro_1694 ,