RetrogeneDB ID: retro_ggor_2644

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:5710690..5711636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSGGOG00000008168
• Aliases: None
• Description: None

Sequence

>retro_ggor_2644
ATGGCGACCTTTGTGAGTGAGCTGGAGGTGGCTAAGCAGAACTTGAGTGAGGCTCTGGGGGACAATGTGAATCAATACTG
GGCTAACTTAAGCTGTGGTTCAAGCGGAAGATCAGGAAAGAGGACTTTGACTTTGAAACTCATAGGCTTCTTTCATAGGA
GAATATGCATTCTCACAATGATTTCCTCCTGGCCATTCTCATGCATTGTCAGATTTTGGTTTCTACATCAGAGGGTGCTG
GATCCTTGCCCTGGATGGGGGGTTCTGCAGCAAAACCTGGAAAGCCCAATGGAAAGAAAAAGTTTTCTTCTGTCAGAAAT
TTGATCATAGATTCCAGCCTCACAATCCTGTCTCAAGAGCCCAGTAATTTGTGGCAAAAGATCCCCAAGATGATGATGAC
TTGAAACTTTGTTCCCACATAATGATGCTTCTCATTCAAGGCTGGCTTGAAGGGAGAAAGACAGTGACTGCTTATGAGCA
TGGGCTGGACAATGTCACCGAGGAGGCTGTTTCAGCTCTTGTCTATGCTGTGGAGAATCACCCTAAAGATATACTGACAT
CAGTTGTGTGAAGAAGGAAAGCTTATCGGTTACGAGATGACCATTTTAAATATGCCTTTGGCAGTAATGTGACCCCACAG
CCGTACCTGAAGAATAATGTAGTAGCTTAGAACAACTTAATATAAAGCCCTCAAGCTTTTACTGCTCCCTGTGCTGGTCA
GAATCCAGCTTCTCACCCACCTCCTGATGAAGCCGAGCAGCAGGCTGCATTCCTGCTGGCATGCTCTGGAGACACTCTAT
CTGCATCTTTATCTCCAGCGAACATGTATGAACTTTTTGAAGCTCTGCGGGTACACAGGGAAGTCATACCTACACATATT
GTCTATGCCGTTAACATTGAAAGGATCATCATGAAAGTCTGGCATCCAAATCATGAAGAGCTGAAG

Alignment

ORF - retro_ggor_2644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 94.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFVSELEAAKKNLSEALGDNVKQYWANL-KLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTR
          MATFVSELE.AK.NLSEALGDNV.QYWANL.KLWFK.KI.KE.FD.E.HRLL...N.HSHNDFLLAIL..
Retrocopy MATFVSELEVAKQNLSEALGDNVNQYWANL<KLWFKRKIRKEDFDFETHRLLS*ENMHSHNDFLLAILMH

Parental  CQILVSTPDGAGSLPWPGGSAAKPG-KPKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKL
          CQILVST..GAGSLPW.GGSAAKPG.K...K.K.....QKFDHRFQP.NP.S.AQ.FVAKDPQDDDDLKL
Retrocopy CQILVSTSEGAGSLPWMGGSAAKPG<KAQWKEKVFFC-QKFDHRFQPHNPVSRAQ*FVAKDPQDDDDLKL

Parental  CSHTMMLPTRGQLEGRMIVTAYEHGLDNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAF
          CSH.MML...G.LEGR..VTAYEHGLDNVTEEAVSA.VYAVENH.KDILTSVV.RRKAYRLRD.HFKYAF
Retrocopy CSHIMMLLIQGWLEGRKTVTAYEHGLDNVTEEAVSALVYAVENHPKDILTSVV*RRKAYRLRDDHFKYAF

Parental  GSNVTPQPYLKNSVVAYNNLIESPPAFTAPCAGQNPASHPPPDDAEQQAALLLACSGDTLPASLPPVNMY
          GSNVTPQPYLKN.VVA.NNLI.SP.AFTAPCAGQNPASHPPPD.AEQQAA.LLACSGDTL.ASL.P.NMY
Retrocopy GSNVTPQPYLKNNVVA*NNLI*SPQAFTAPCAGQNPASHPPPDEAEQQAAFLLACSGDTLSASLSPANMY

Parental  DLFEALQVHREVIPTHTVYALNIERIITKLWHPNHEELQ
          .LFEAL.VHREVIPTH.VYA.NIERII.K.WHPNHEEL.
Retrocopy ELFEALRVHREVIPTHIVYAVNIERIIMKVWHPNHEELK

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	16.11 RPM
SRP007412_cerebellum	0.00 RPM	12.65 RPM
SRP007412_heart	0.00 RPM	2.31 RPM
SRP007412_kidney	0.00 RPM	8.06 RPM
SRP007412_liver	0.00 RPM	6.07 RPM
SRP007412_testis	0.00 RPM	14.92 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2644 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3928
Pan troglodytes	retro_ptro_2671
Pongo abelii	retro_pabe_3243

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644 ,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,