RetrogeneDB ID: retro_ggor_2906

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:52448735..52450564(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022085
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSPT1
• Ensembl ID: ENSGGOG00000004071
• Aliases: None
• Description: None

Sequence

>retro_ggor_2906
ATGGAAGCCCCGGGGTCGGCCCCGAGCGGGGATGGAGTCTCCTCTGCGGTGGCCGAGGNNNNNNNNNNNNNNNNCCCAGC
TCGGCTTTCAGCCGTCAGCTCAACGTCAACGCCAAGCCCTTCGTGCCTAACGTACACGCCGCGGAGTTCGTGCCGTCCTT
CCTGCGGGGCCCGACTCAGCCGCCCACCCTCCCGGCCGGCTCCGGCAGCAACGATGAAACCTGCACCGGCGCGGGATACC
CTCAAGGTAAAAGGATGGGACGGGGGGCACCTGTGGAACCTTCCCGAGAGGAACCGTTAGTGTCGCTTGAAGGTTCCAAT
TCAGCCGTTACCATGGAACTTTCAGAACCTGTTGTAGAAAATGGAGAGGTGGAAATGGCCCTAGAAGAATCATGGGAGCA
CAGTAAAGAAGTAAGTGAAGCCGAGCCTGGGGGTGGTTCCTCGGGAGATTCAGGGCCCCCAGAAGAAAGTGGCCAGGAAA
TGATGGAGGAAAAAGAGGAAATAAGAAAATCCAAATCTGTGATCGTACCCTCAGGTGCACCTAAGAAAGAACACGTAAAT
GTAGTATTCATTGGCCATGTAGACGCTGGCAAGTCAACCATCGGAGGACAGATAATGTTTTTGACTGGAATGGTTGACAA
AAGAACACTGGAGAAATATGAAAGAGAAGCTAAGGAAAAAAACAGAGAAACCTGGTATTTGTCCTGGGCCTTAGATACAA
ATCAGGAGGAACGAGACAAGGGTAAAACAGTCGAAGTGGGTCGTGCCTATTTTGAAACAGAAAGGAAACATTTCACAATT
TTAGATGCCCCTGGCCACAAGAGTTTTGTCCCAAATATGATTGGTGGTGCTTCTCAAGCTGATTTGGCTGTGCTGGTCAT
CTCTGCCAGGAAAGGAGAGTTTGAAACTGGATTTGAAAAAGGTGGACAGACAAGAGAACATGCGATGTTGGCAAAAACGG
CAGGGGTAAAACATTTAATAGTGCTTATTAATAAGATGGATGATCCCACAGTAAATTGGAGCATTGAGAGATATGAAGAA
TGTAAAGAAAAACTGGTGCCCTTTTTGAAAAAAGTAGGCTTCAGTCCAAAAAAGGACATTCACTTTATGCCCTGCTCAGG
ACTGACCGGAGCAAATATTAAAGAGCAGTCAGATTTCTGCCCTTGGTACACTGGATTACCATTTATTCCGTATTTGGATA
ACTTGCCAAACTTCAACAGATCAATTGATGGACCAATAAGACTGCCAATTGTGGATAAGTACAAAGATATGGGCACTGTG
GTCCTGGGAAAGCTGGAATCCGGGTCCATTTTTAAAGGCCAGCAGCTCGTGATGATGCCAAACAAGCACAATGTAGAAGT
TCTTGGAATACTTTCTGATGATACTGAAACTGATTTTGTAGCCCCAGGTGAAAACCTCAAAATCAGACTGAAGGGAATTG
AAGAAGAAGAGATTCTTCCAGGATTCATACTTTGTGATCCTAGTAACCTCTGCCATTCTGGACGCACGTTTGATGTTCAG
ATAGTGATTATTGAGCACAAATCCATCATCTGCCCAGGTTATAATGCGGTGCTGCACATTCATACTTGTATTGAGGAAGT
TGAGATAACAGCGTTAATCTCCTTGGTAGACAAAAAATCAGGAGAAAAAAGTAAGACACGACCCCGCTTCGTGAAACAAG
ATCAAGTATGCATTGCTCGTTTAAGGACAGCAGGAACCATCTGCCTCGAGACGTTCAAAGATTTTCCTCAGATGGGTCGT
TTTACTTTAAGAGATGAGGGTAAGACCATTGCAATTGGAAAAGTTCTGAAACTGGTCCCGGAGAAGGAC

Alignment

ORF - retro_ggor_2906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAPGPGPCG-GGGSLAAAAEAQRENLSAAFSRQLNVNAKPFVPNVHAAEFVPSFLRGPAAPPP-PAGGA
          MEAPG..P.G.G...L...........S.AFSRQLNVNAKPFVPNVHAAEFVPSFLRGP..PP..PAG..
Retrocopy MEAPGSAPSG<GWSLLCGGRXXXXXXPSSAFSRQLNVNAKPFVPNVHAAEFVPSFLRGPTQPPTLPAGSG

Parental  ANNH---GAGSGAG---GPAAPVESSQEEQSLC-EGSNSAVSMELSEPIVENGETEMSPEESWEHKEEIS
          .N.....GAG...G...G..APVE.S.EE.....EGSNSAV.MELSEP.VENGE.EM..EESWEH..E.S
Retrocopy SNDETCTGAGYPQGKRMGRGAPVEPSREEPLVSLEGSNSAVTMELSEPVVENGEVEMALEESWEHSKEVS

Parental  EAEPGGGSLGDGRPPEESAHEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLT
          EAEPGGGS.GD..PPEES..EMMEE.EEI.K.KSV..P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LT
Retrocopy EAEPGGGSSGDSGPPEESGQEMMEEKEEIRKSKSVIVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLT

Parental  GMVDKRTLEKYEREAKEKNRETWYRYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFV
          GMVDKRTLEKYEREAKEKNRETWY..LSWALDTNQEERDKGKTVEVGRAYFETE.KHFTILDAPGHKSFV
Retrocopy GMVDKRTLEKYEREAKEKNRETWY--LSWALDTNQEERDKGKTVEVGRAYFETERKHFTILDAPGHKSFV

Parental  PNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEE
          PNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWS.ERYEE
Retrocopy PNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSIERYEE

Parental  CKEKLVPFLKKVGFNPKKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPI
          CKEKLVPFLKKVGF.PKKDIHFMPCSGLTGAN.KEQSDFCPWY.GLPFIPYLDNLPNFNRS.DGPIRLPI
Retrocopy CKEKLVPFLKKVGFSPKKDIHFMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNLPNFNRSIDGPIRLPI

Parental  VDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILP
          VDKYKDMGTVVLGKLESGSI.KGQQLVMMPNKHNVEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILP
Retrocopy VDKYKDMGTVVLGKLESGSIFKGQQLVMMPNKHNVEVLGILSDDTETDFVAPGENLKIRLKGIEEEEILP

Parental  GFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRF
          GFILCDP.NLCHSGRTFD.QIVIIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRF
Retrocopy GFILCDPSNLCHSGRTFDVQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRF

Parental  VKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
          VKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
Retrocopy VKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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	14.48 RPM	46.08 RPM
SRP007412_cerebellum	11.03 RPM	42.75 RPM
SRP007412_heart	1.66 RPM	15.10 RPM
SRP007412_kidney	5.56 RPM	61.13 RPM
SRP007412_liver	6.17 RPM	40.75 RPM
SRP007412_testis	19.79 RPM	89.20 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_2906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2906 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009589	1 retrocopy	retro_amel_4,
Bos taurus	ENSBTAG00000003577	2 retrocopies	retro_btau_1793, retro_btau_1840,
Canis familiaris	ENSCAFG00000018856	1 retrocopy	retro_cfam_2072,
Callithrix jacchus	ENSCJAG00000018191	1 retrocopy	retro_cjac_618,
Cavia porcellus	ENSCPOG00000009381	1 retrocopy	retro_cpor_73,
Equus caballus	ENSECAG00000021195	1 retrocopy	retro_ecab_739,
Echinops telfairi	ENSETEG00000018249	1 retrocopy	retro_etel_1626,
Felis catus	ENSFCAG00000022281	1 retrocopy	retro_fcat_1913,
Gorilla gorilla	ENSGGOG00000004071	1 retrocopy	retro_ggor_2906 ,
Microcebus murinus	ENSMICG00000014137	1 retrocopy	retro_mmur_28,
Myotis lucifugus	ENSMLUG00000000792	1 retrocopy	retro_mluc_98,
Macaca mulatta	ENSMMUG00000023178	1 retrocopy	retro_mmul_118,
Monodelphis domestica	ENSMODG00000004728	1 retrocopy	retro_mdom_1420,
Mustela putorius furo	ENSMPUG00000014504	1 retrocopy	retro_mputfur_147,
Mus musculus	ENSMUSG00000062203	1 retrocopy	retro_mmus_238,
Nomascus leucogenys	ENSNLEG00000010199	1 retrocopy	retro_nleu_2705,
Oryctolagus cuniculus	ENSOCUG00000004759	1 retrocopy	retro_ocun_1664,
Otolemur garnettii	ENSOGAG00000007083	1 retrocopy	retro_ogar_100,
Pteropus vampyrus	ENSPVAG00000005009	1 retrocopy	retro_pvam_1426,
Rattus norvegicus	ENSRNOG00000002335	1 retrocopy	retro_rnor_2931,
Sarcophilus harrisii	ENSSHAG00000005908	1 retrocopy	retro_shar_14,
Ictidomys tridecemlineatus	ENSSTOG00000015406	1 retrocopy	retro_itri_109,
Tupaia belangeri	ENSTBEG00000008873	2 retrocopies	retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta	ENSTSYG00000013812	2 retrocopies	retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus	ENSTTRG00000011630	1 retrocopy	retro_ttru_12,