RetrogeneDB ID: retro_ggor_2585

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:38283436..38284263(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024680
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSGGOG00000010233
• Aliases: None
• Description: None

Sequence

>retro_ggor_2585
ATGGTGGCCGAGTTGGAGTATGAGTCTGTGCTGTGTGTGAAGCCAAACGTCAGCGTCTACTGGATTCCTCCCTGGGCCTC
CAACTGTGATTACAGGGCATCTGACTGGAAATTAGGCCAGCCTGATTGGACTGGTCACCTCCGAATCATTTCAAAAGGGA
AGACTGCCTATATCAAACTCAAGGATAAAGTTTCAGGGGAGCTCTTCACTCAGACACCAGTAGAGCAATATCCTGGTATT
GCTGTGGAGACCGTGACAGATTCCAGCTGCTACTTTTCAATCTGGATTCAGGATGGTCCTGGGCAGAGTGCTGTCATTGA
CACTGCTGGCTTCACAGATCGGGGAGATGCCTTTGACTTTAATGTCTCCTTGCAGGATCACTTCAAATGGGTAAAGCAGG
AATCTGAGATTTCCAAGGAATTTCAAGAAATGGACGCTTGTCCTAACTTGGATCTGGGCTTCAAAGAAAGACAAACCATC
AAGTTGAGTATGGGGAACATTACAACCAAGAATGGAGGTGCTTCTAAGCCCAGGACTGCAATGGGTGGGGGCCTGAGCTT
ACTCGCATCCCTGCCAGGAGGCCAAGTCAGTATTCCCTCACTGTCCTCCTCAGTTGCATCAGCAATCATGTCACCCCACC
AGCCATTCCAAAATCTAACCATGGAGGCAGTGATGCAGATATCCTTTTAGATTTGGATTCTCCTGCTCCTGTCACAACAC
CAGCACCAACTCCAGTTTCTGCAAGCAATGACTTGTGGGGAGACTTCAGCACTGCATCCAGCTCTGTTCCAAACCAGGCA
CCACAGCCATCCAACTGGGTCCAGTTC

Alignment

ORF - retro_ggor_2585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATELEYESVLCVKPDVSVYRIPPRASNRGYSPRASDWKLDQPDWTGRLRITSRGKTAYIKLEDKVSGEL
          M..ELEYESVLCVKP.VSVY.IPP.ASN..Y..RASDWKL.QPDWTG.LRI.S.GKTAYIKL.DKVSGEL
Retrocopy MVAELEYESVLCVKPNVSVYWIPPWASNCDY--RASDWKLGQPDWTGHLRIISKGKTAYIKLKDKVSGEL

Parental  FAQAPVEQYPGIAVETVTDSSRYFVIRIQDGTGRSAFIGI-GFTDRGDAFDFNVSLQDHFKWVKQESEIS
          F.Q.PVEQYPGIAVETVTDSS.YF.I.IQDG.G.SA.I...GFTDRGDAFDFNVSLQDHFKWVKQESEIS
Retrocopy FTQTPVEQYPGIAVETVTDSSCYFSIWIQDGPGQSAVIDTAGFTDRGDAFDFNVSLQDHFKWVKQESEIS

Parental  KESQEMDARPKLDLGFKEGQTIKLSIGNITNKKGGASKPRTARGGGLSLLPPPPGGKVTIPPPSSSVA-I
          KE.QEMDA.P.LDLGFKE.QTIKLS.GNIT.K.GGASKPRTA.GGGLSLL...PGG.V.IP..SSSVA.I
Retrocopy KEFQEMDACPNLDLGFKERQTIKLSMGNITTKNGGASKPRTAMGGGLSLLASLPGGQVSIPSLSSSVA<I

Parental  SNHVTPPPIPKSNHGGSDADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF
          SNHVTPP.IPKSNHGGSDADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF
Retrocopy SNHVTPPAIPKSNHGGSDADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF

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	0.10 RPM	126.31 RPM
SRP007412_cerebellum	0.16 RPM	87.78 RPM
SRP007412_heart	0.00 RPM	5.69 RPM
SRP007412_kidney	0.00 RPM	27.11 RPM
SRP007412_liver	0.00 RPM	20.36 RPM
SRP007412_testis	0.00 RPM	42.79 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_2585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585 ,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,