RetrogeneDB ID: retro_ggor_1752

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:130970757..130971423(+)
• Located in intron of: ENSGGOG00000004259

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD5
• Ensembl ID: ENSGGOG00000010496
• Aliases: None
• Description: None

Sequence

>retro_ggor_1752
CTGCCACCTGCCTGGGGCAGCCTTAGGGCAGGGCTGGCGGGGGCGACCTGTGCTGCTGCAGTGCAAGACTCAGAGTGCCG
TGGCCCAGCACCCGGTAGCTTGTCCAAATGGCTCTGGCTCAACATTGGTGGCACCTACTTTCTCACCACCCAGCAGATGC
TGTGCCAGGACCTGAAATACTTCCTGTACTCCTTGTATCAGGCTAACCCCGACAAGGATGAAACTGTTGCCTATTTAATG
GGCAGAGACCCCACCTATTTTGGGCCTGTGCTGAACTACCTGAGACGTGGCAAGCTGGTGATTAACAAAGACCTTGTGGA
GGAAGGAGTGTTGGAAAAAGCAGAATTTTACAGTATCACTTCATTAATAAAACTTGTAAAGGACAAAATTAGAGAACAAG
AGAGCAAAACATCACAGGTGCCCATGAAGCATGTGTACCACGTGCTTCAGTGTCAGGAGGAGGAACTCACACAGGTGGTG
TCCACCATGTCCGACAGCTGGAAGTTTGAACAACTGGTCAGCAATGGCTCTTCTTACAACTATGGGAATGAAGATCAGGC
CAAGTTCCTCTATGTGGTGTCCAAGGAACTTCACAACACCCCATACAGTATGGCCAGTGAACCCAGCAAGAAGGCCAAGA
TTTTGCAAGAACAAGGTTCAAGGATG

Alignment

ORF - retro_ggor_1752 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.78 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSPARGGIGAGLGGGLCRRCSAGLGALAQRPGSVSKWVRLNVGGTYFLTTRQTLCRDPKSFLYRLCQADP
          L.PA.G...AGL.G..C.............PGS.SKW..LN.GGTYFLTT.Q.LC.D.K.FLY.L.QA.P
Retrocopy LPPAWGSLRAGLAGATCAAAVQDSECRGPAPGSLSKWLWLNIGGTYFLTTQQMLCQDLKYFLYSLYQANP

Parental  DLDSDKDETGAYLIDRDPTYFGPVLNYLRHGKLVINKDLAEEGVLEEAEFYNITSLIKLVKDKIRERDSK
          ....DKDET.AYL..RDPTYFGPVLNYLR.GKLVINKDL.EEGVLE.AEFY.ITSLIKLVKDKIRE..SK
Retrocopy ----DKDETVAYLMGRDPTYFGPVLNYLRRGKLVINKDLVEEGVLEKAEFYSITSLIKLVKDKIREQESK

Parental  TSQVPVKHVYRVLQCQEEELTQMVSTMSDGWKFEQLVSIGSSYNYGNEDQAEFLCVVSKELHNTPYGTAS
          TSQVP.KHVY.VLQCQEEELTQ.VSTMSD.WKFEQLVS.GSSYNYGNEDQA.FL.VVSKELHNTPY..AS
Retrocopy TSQVPMKHVYHVLQCQEEELTQVVSTMSDSWKFEQLVSNGSSYNYGNEDQAKFLYVVSKELHNTPYSMAS

Parental  EPSEKAKILQERGSRM
          EPS.KAKILQE.GSRM
Retrocopy EPSKKAKILQEQGSRM

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	0.05 RPM	12.71 RPM
SRP007412_cerebellum	0.16 RPM	18.12 RPM
SRP007412_heart	0.00 RPM	5.35 RPM
SRP007412_kidney	0.04 RPM	11.29 RPM
SRP007412_liver	0.05 RPM	8.73 RPM
SRP007412_testis	0.73 RPM	17.51 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_1752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1752 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2224
Pan troglodytes	retro_ptro_1685
Pongo abelii	retro_pabe_2093

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019357	1 retrocopy	retro_cfam_433,
Homo sapiens	ENSG00000167977	1 retrocopy	retro_hsap_2224,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752 ,
Monodelphis domestica	ENSMODG00000016596	1 retrocopy	retro_mdom_506,
Sarcophilus harrisii	ENSSHAG00000006867	1 retrocopy	retro_shar_158,
Ictidomys tridecemlineatus	ENSSTOG00000006647	8 retrocopies	retro_itri_1562, retro_itri_1690, retro_itri_1692, retro_itri_1761, retro_itri_1779, retro_itri_1844, retro_itri_1889, retro_itri_950,
Tursiops truncatus	ENSTTRG00000008237	1 retrocopy	retro_ttru_1510,