RetrogeneDB ID: retro_ggor_2609

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:85747898..85748813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSGGOG00000027535
• Aliases: None
• Description: None

Sequence

>retro_ggor_2609
CTAAGAAGGAGAAATATAAGCTCATTTACTGATGATGCTACTTCTCCACTGCAGAAGAACTGCAACAACCAGGATACTGT
AAATTGGTCTGTTGATGACGTTGTCAAAGGTATAAATAACAACAATGTGGAAAGTCAGCTGTAAGCTACTCAAGCTGCCA
GGAAACTACCTTCTGGAGAAAACCAGCTCCCCTCACAGACAACATAATCCAGGCTGGTTTGATTCCAACATTTCTGTCCT
TCTTGGGAAGAACTGACTGTAGTCCCATTCAGTTTGAATCTGCTTGGGCACTCACTAACATTGCTTCTGGGGCATCAGAA
CAGACCAAGGCTGTGGTAGACGGAGGTGCCATCCCAGCATTCATTTCTCTGTTGGCATCTCCCCATGCTCACATCAGTGA
ACAAGCTGTATGGGCTGTAGGAAACATTGCAGGTGATGGTTCCATTTTCGGAGACTTGGTTATCAACTGCGGTGCAGTTG
ACCCACTGTTGGCTCTTCTTGCAGTTCCTGATATGTCATCTTTAGCATGCGATTACTTAAGTAATCTTATGTGGACATTT
TCAAACCTTTGCCGCAAGAATACTAGCACCTCCTTTAGATTCTGTTGAGCAAATTTTTCCTACGTTAGTTTGATTCCTGC
ATCACGATGATCCAGAAATATTAGCAGATATCTGCTAGGTTATTCCTTACCTTTCTGGTGGTCCAAATGAATGAATTGAC
ATGGTCGTGAAAACGGGAGTTTTGCCCCAACTTGTGAAGTCTCTAGGAGCTTCCGAATTGCCATTTGTGACTCCAGCACT
AAGAGCCATTGGGAATATTGTCACTGGTACAGATGAACAGACTCAGGTTGTGATCAATGCAGGAGCACTCACCGTCTTTC
CTAGCCTGCTAATCAACCCCAAAACTAACAGTCAA

Alignment

ORF - retro_ggor_2609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 57.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKRRNVSSFPDDATSPLQENRNNQGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSRE-KQPPI-DNI
          L.RRN.SSF.DDATSPLQ.N.NNQ.TVNWSVDD.VKGIN..NVE.QL.ATQAARKL.S.E.K..P..DNI
Retrocopy LRRRNISSFTDDATSPLQKNCNNQDTVNWSVDDVVKGINNNNVESQL*ATQAARKLPSGE<KPAPLTDNI

Parental  IRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWA
          I.AGLIP.F.SFLGRTDCSPIQFESAWALTNIASG.SEQTKAVVDGGAIPAFISLLASPHAHISEQAVWA
Retrocopy IQAGLIPTFLSFLGRTDCSPIQFESAWALTNIASGASEQTKAVVDGGAIPAFISLLASPHAHISEQAVWA

Parental  LGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNP-APPIDAVEQILP
          .GNIAGDGS.F.DLVI..GAVDPLLALLAVPDMSSLAC.YL.NL.WT.SNLCR.KN..APP.D.VEQI.P
Retrocopy VGNIAGDGSIFGDLVINCGAVDPLLALLAVPDMSSLACDYLSNLMWTFSNLCR-KNT>APPLDSVEQIFP

Parental  TLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGT
          TLV..LHHDDPE.LAD.C..I.YL..GPNE.I.MVVKTGV.PQLVK.LGASELP.VTPALRAIGNIVTGT
Retrocopy TLV*FLHHDDPEILADIC*VIPYLSGGPNE*IDMVVKTGVLPQLVKSLGASELPFVTPALRAIGNIVTGT

Parental  DEQTQVLIDAGALAVFPSLLTNPKTNIQ
          DEQTQV.I.AGAL.VFPSLL.NPKTN.Q
Retrocopy DEQTQVVINAGALTVFPSLLINPKTNSQ

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	22.06 RPM
SRP007412_cerebellum	0.00 RPM	7.49 RPM
SRP007412_heart	0.00 RPM	2.66 RPM
SRP007412_kidney	0.00 RPM	13.82 RPM
SRP007412_liver	0.00 RPM	4.54 RPM
SRP007412_testis	0.00 RPM	215.90 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_2609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2609 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1635

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609 ,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,