RetrogeneDB ID: retro_ggor_2197

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:98609497..98611112(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000014116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSGGOG00000024064
• Aliases: None
• Description: None

Sequence

>retro_ggor_2197
ATGGCATCCATGGGAACCCTCGCCTTTGATGAATATGGGCACCCTTTCCTCATCATCAAGGATCAGGACCACAAGTCCTG
TCTTATGGGACTGAGGCCCTTAAGTCTCATATAGTGGCAGAAAAGGCTGTAGCAAATATGATGAGAACATCACTTGGGCC
AAATGGGCTTGATAAGATGATGGTGGATAAGGATGGTGATATGACTGTAGCTAATGATGGGTCCCCATCTTAAGCATGAT
GGATGTCGATCATCAGATTGCTAAGCTGATGGTGGAACTGTCCAAGTCTCAGGATGATGAAATTGGACTTGGAACCACAG
GAGTGGTAGTCCTGGCTGCTGACTTGTTAGAAGAAGCCAAGCAGTTGCTAGACTGAGGCATTCACCCAATCAGAATAGCT
GATGGTTATGAGCAGGCTGCCAGCATTGCTGTTGAACACCTGGACAAGATCAGTCATAGTGTTCTTGTTGACATAAAGGA
CACTGAACCCCTGATTCCGACTGCAAAAACCATGCTGGGCTCCAAAGTGGTCAAAGTTGGCACCAACAAATGGCTGAGAT
TGCTGTGAATGCTGTCCTCACTGTAGCAGATATGGAGCGGAGAGATACTGACTTTGAGCTCGTCAACGTAGAAGGCAAAG
TGGGCGGGAGGCTGGAGGACACAAAACTGATCAAGGGCGTGATTGTGGACAAGGATTTCCAGTCACCTATAGGTGCCGAA
AAAAGTGGAAGATGCTAAGATTGCAATTCTCACATGTCCATTTGAACCACCCAAGCCAAAAACAAAGCATAAGCTGGATG
TGACCTCCATAGATCATAAAGCTCTTCACAAATATGAAAAGGAGAAATTTGAAGAGATGATTCAACAAATTAAAGAGACT
GGTGCTAACCTAGCAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTATTTCTTCAGAACAACTTGCCTGTGGT
TTGCTGGGTAGGGGGACTTGAAATTGAACTGATTGCCATCTCAACAAGAGGGCAGATTGTCCCAGGTTCTCAGAGCTCAC
GGCCAAGATGCTGGGCTTTACCGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAATGCTGGTCATCGAGC
AGTGTAAGAACTCCAGAGCTGTAACCATTTTTATCAGAGGAGGAAATAAGATGATCATTGAGGAGGTGAAACGATCCCTT
CACGATGTTTTGTGTGTCATCAGCAACCTCATCCGCGATAATCCTGTGGCATACGGAGGAGGGTTTGCTGAGATATCCCG
TGCTCTGGCAGTTAGCCAAGAGGCGGATAAGTGCCCCACCTTAGACCAGTACACCATAAAAGCGTTTGCCGAACCTCTGG
AGTTGCCCCATGGCCCTTTCTGAAAACAGTGGCATGAATCCCATCCAGACTATGACAGAAGTCCGAGCCAGACAAGTGAA
GGAGATGAACCCTGCTCTCGGTACTGACTGTTTGCACAAGGGGACAAATGATATGAAGCAACAGCATGTCATAGAAATTT
TGACTGGCAAAAAGCAACAGACATCTTTCACAACACAAATGGTTAGAATGATTTTGAAGACTGACGACATTCATAAGCCT
GGAGAATCTGAAGAA

Alignment

ORF - retro_ggor_2197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MASMGTLAFDEYGRPFLIIKDQDRKSRLMGL-EALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVT
          MASMGTLAFDEYG.PFLIIKDQD.KS.LMGL.EALKSHI.A.KAVAN.MRTSLGPNGLDKMMVDKDGD.T
Retrocopy MASMGTLAFDEYGHPFLIIKDQDHKSCLMGL<EALKSHIVAEKAVANMMRTSLGPNGLDKMMVDKDGDMT

Parental  VTNDGAT-ILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYE
          V.NDG...ILSMMDVDHQIAKLMVELSKSQDDEIG.GTTGVVVLA..LLEEA.QLLD.GIHPIRIADGYE
Retrocopy VANDGSP<ILSMMDVDHQIAKLMVELSKSQDDEIGLGTTGVVVLAADLLEEAKQLLD*GIHPIRIADGYE

Parental  QAARVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVN-SCHRQMAEIAVNAVLTVADMERRDVDFE
          QAA..A.EHLDKIS.SVLVDIKDTEPLI.TAKT.LGSKVV..S.H.QMAEIAVNAVLTVADMERRD.DFE
Retrocopy QAASIAVEHLDKISHSVLVDIKDTEPLIPTAKTMLGSKVVK<SWHQQMAEIAVNAVLTVADMERRDTDFE

Parental  LIKVEGKVGGRLEDTKLIKGVIVDKDF-SHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKA
          L..VEGKVGGRLEDTKLIKGVIVDKDF.SH...PKKVEDAKIAILTCPFEPPKPKTKHKLDVTS..D.KA
Retrocopy LVNVEGKVGGRLEDTKLIKGVIVDKDF>SHL*VPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSI-DHKA

Parental  LQKYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVP-RF
          L.KYEKEKFEEMIQQIKETGANLAICQWGFDDEANHL.LQNNLP.V.WVGG.EIELIAI.T.G.IVP.RF
Retrocopy LHKYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLFLQNNLPVVCWVGGLEIELIAISTRGQIVP<RF

Parental  SELTAEKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRD
          SELTA..LGF.GLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEE.KRSLHD.LCVI.NLIRD
Retrocopy SELTAKMLGFTGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEVKRSLHDVLCVISNLIRD

Parental  NRVVYGGGAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIP-MALSENSGMNPIQTMTEVRARQVKE
          N.V.YGGG.AEIS.ALAVSQEADKCPTL.QY...AFA..LE..P.MALSENSGMNPIQTMTEVRARQVKE
Retrocopy NPVAYGGGFAEISRALAVSQEADKCPTLDQYTIKAFAEPLE-LP>MALSENSGMNPIQTMTEVRARQVKE

Parental  MNPALGIDCLHKGTNDMKQQHVIETLIGKKQQISLATQMVRMILKIDDIRKPGESEE
          MNPALG.DCLHKGTNDMKQQHVIE.L.GKKQQ.S..TQMVRMILK.DDI.KPGESEE
Retrocopy MNPALGTDCLHKGTNDMKQQHVIEILTGKKQQTSFTTQMVRMILKTDDIHKPGESEE

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	82.05 RPM
SRP007412_cerebellum	0.08 RPM	51.97 RPM
SRP007412_heart	0.00 RPM	22.67 RPM
SRP007412_kidney	0.00 RPM	104.10 RPM
SRP007412_liver	0.00 RPM	53.07 RPM
SRP007412_testis	0.21 RPM	334.63 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_2197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2197 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3230
Pan troglodytes	retro_ptro_2182
Pongo abelii	retro_pabe_2678
Macaca mulatta	retro_mmul_2033

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017889	1 retrocopy	retro_btau_1432,
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516,
Homo sapiens	ENSG00000150753	2 retrocopies	retro_hsap_1219, retro_hsap_3230,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197 ,
Myotis lucifugus	ENSMLUG00000007977	1 retrocopy	retro_mluc_1735,
Macaca mulatta	ENSMMUG00000020112	2 retrocopies	retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,