RetrogeneDB ID: retro_ptro_3208

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:46914741..46916327(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNBL1
• Ensembl ID: ENSPTRG00000023688
• Aliases: CTNNBL1, PDGFRA
• Description: Pan troglodytes catenin, beta like 1 (CTNNBL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246652]

Sequence

>retro_ptro_3208
ATGGACATGGGCAAACTTCTGAGCTACCAGCCCAACAGGGGCATAAAACGTCCCCGAGATGGCAAAGAGGAGGAGCAGAA
GATGCATCGGAAACAAACTAGTACTCAAGATTGGGAAGAGGAAATGATTGTGGTGGAAGAAGCAAAGGATGACAAAAATT
TGCTGCTTCAGATTATTGACACAGAGGGTGAGGAGGAAGAGAAAGAGGAGGAGCCATTGGATGAAAGCTCAGTGAAGAAA
ATGATCCTTGCATTTGAATAGTGAGCATATAAAAACCAAGAATTGCAGATTAAGTTTCCAGACAATCCAGAGAAGTTCAT
GGAATCCCAACTGGACCTACATGACATCATTCAGAAGATGCACTTGGTGGCCACCATGCCAGACCTGTACCTTTTGCTGG
AGCTGAATGCTGTGCAGTCACTTCTTGGTTTGCTTGGACACAATAATACAGACGTGTCCATAGCTGGGGTTGATTTGAGT
CAGGAATTAACAGATATAGACATCTTCTATGAGAGCAGAGAGGGAGCAGAAGTACTCATTGATGCTCTGGTGGATGGGCA
GGTGATAGCGCTGCTGGTGCAGAACGTGGAGCGCCTGGATGAGTCTGTGAAGGAGCAGGTCAATGGTGCCCATAACACTC
TTGTTATTGTGGAAAACATGGCTGAGTTCTAGCTGGAGATGTGTACAAAAGATGCCCAGCAGGGTCTTCCTCAGTGGCTG
TTGAAGAGGCTGAAGGCAAAGAAGCCTTTTGATGCCAACAAACTGTATTGCAGTGAAATGCAGGCCATATTGCTCCAGGA
CAATGATGAAAACAGGAAATTGCTTGGGGAGCTGGATAGAATTGATGCACTTCTTCACAGTTATCTGTGTTTAAAAGACA
CAATCCCAGCACAGCAAAGGAGCAGGAGATGATGGAGAATCTGTTTGATTCACTCTGCTTCTAACTAATGCTCACTTCCA
ATCGTGAGCACTTCCTGAAGGGCGAGGGTCTTCAGGTGATGAATCTCATGCTCAGGGAAAAGAAGATCTCACGGAGCAGG
GTCCTGAAAGTGCTGATTGCACCCGAGGGCATCTACAACTGCGGTAAATTTGTTGACATTCTTGGCTTATGAACCATCTT
TCCCCTCTTTATGGAATTTCCCAGGAAGATCAAGAAAGTGGGTACCACTGACAAGGAACACAAACAGCATGTCTGTTCCA
TTCTGGCTTCCCTTTTGTGGAACCTGAGAGGGCATCAGTGAACCCGGCTTCTGAATAAATTCACTGAAAATGACAGTGAG
TAGGCTGACAGACTAATGGAGTTGCATTTTCAATATCTGGGTGCAATGCAGGTGGCAGACAAGAGGAATGAAGGGGAAAA
ACATGACATGGTCCAGCGTGGAGAGATCATAGACAGTGACATGGGGGATGAGTTCTACCTCCAGTGCTTGGATGCAGAGC
TGTTTGTTCTCCAGTGCATCTGCTGCATTATGTCCAAGATCTGCAATGCCAATGTCCCCCAGATTTGCCAGAGGGTTCAC
CAGATCCTAAACATGTGAGGACGCTCCATCAAAATTGTCAGGCATATTATCAAGGGGTATGCGGAG

Alignment

ORF - retro_ptro_3208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 95.56 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDVGELLSYQPNRGTKRPRDDEEEEQKMRRKQTGTRERGRYREEEMTVVEEADDDKKRLLQIIDRDGEEE
          MD.G.LLSYQPNRG.KRPRD..EEEQKM.RKQT.T.......EE.M.VVEEA.DDK..LLQIID..GEEE
Retrocopy MDMGKLLSYQPNRGIKRPRDGKEEEQKMHRKQTSTQD---WEEE-MIVVEEAKDDKNLLLQIIDTEGEEE

Parental  EEEEEPLDESSVKKMILTFEKRSYKNQELRIKFPDNPEKFMESELDLNDIIQEMHVVATMPDLYHLLVEL
          E.EEEPLDESSVKKMIL.FE...YKNQEL.IKFPDNPEKFMES.LDL.DIIQ.MH.VATMPDLY.LL.EL
Retrocopy EKEEEPLDESSVKKMILAFE**AYKNQELQIKFPDNPEKFMESQLDLHDIIQKMHLVATMPDLY-LLLEL

Parental  NAVQSLLGLLGHDNTDVSIAVVDLLQELTDIDTLHESEEGAEVLIDALVDGQVVALLVQNLERLDESVKE
          NAVQSLLGLLGH.NTDVSIA.VDL.QELTDID...ES.EGAEVLIDALVDGQV.ALLVQN.ERLDESVKE
Retrocopy NAVQSLLGLLGHNNTDVSIAGVDLSQELTDIDIFYESREGAEVLIDALVDGQVIALLVQNVERLDESVKE

Parental  EADGVHNTLAIVENMAEFRPEMCTEGAQQGLLQWLLKRLKAKMPFDANKLYCSEVLAILLQDNDENRELL
          ...G.HNTL.IVENMAEF..EMCT..AQQGL.QWLLKRLKAK.PFDANKLYCSE..AILLQDNDENR.LL
Retrocopy QVNGAHNTLVIVENMAEF*LEMCTKDAQQGLPQWLLKRLKAKKPFDANKLYCSEMQAILLQDNDENRKLL

Parental  GELDGIDVLL-QQLSVFKRHNPSTAEEQEMMENLFDSLCSCLMLSSNRERFLKGEGLQLMNLMLREKKIS
          GELD.ID.LL..QLSVFKRHNPSTA.EQEMMENLFDSLC..LML.SNRE.FLKGEGLQ.MNLMLREKKIS
Retrocopy GELDRIDALL<SQLSVFKRHNPSTAKEQEMMENLFDSLCF*LMLTSNREHFLKGEGLQVMNLMLREKKIS

Parental  RSSALKVLDHAMIGPEGTDNCHKFVDILGLRTIFPLFMKSPRKIKKVGTTEKEHEEHVCSILASLLRNLR
          RS..LKVL....I.PEG..NC.KFVDILGL.TIFPLFM..PRKIKKVGTT.KEH..HVCSILASLL.NLR
Retrocopy RSRVLKVL----IAPEGIYNCGKFVDILGL*TIFPLFMEFPRKIKKVGTTDKEHKQHVCSILASLLWNLR

Parental  GQQRTRLLNKFTENDSEKVDRLMELHFKYLGAMQVADKKIEGEKHDMVRRGEIIDNDTEEEFYLRRLDAG
          G.Q.TRLLNKFTENDSE..DRLMELHF.YLGAMQVADK..EGEKHDMV.RGEIID.D...EFYL..LDA.
Retrocopy GHQ*TRLLNKFTENDSE*ADRLMELHFQYLGAMQVADKRNEGEKHDMVQRGEIIDSDMGDEFYLQCLDAE

Parental  LFVLQHICYIMAEICNANVPQIRQRVHQILNMRGSSIKIVRHIIKEYAE
          LFVLQ.IC.IM..ICNANVPQI.QRVHQILNM.G.SIKIVRHIIK.YAE
Retrocopy LFVLQCICCIMSKICNANVPQICQRVHQILNM*GRSIKIVRHIIKGYAE

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	28.74 RPM
SRP007412_cerebellum	0.00 RPM	36.78 RPM
SRP007412_heart	0.00 RPM	27.37 RPM
SRP007412_kidney	0.00 RPM	26.18 RPM
SRP007412_liver	0.00 RPM	30.54 RPM
SRP007412_testis	0.00 RPM	59.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3208 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3208 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4819
Gorilla gorilla	retro_ggor_3003
Pongo abelii	retro_pabe_3747
Macaca mulatta	retro_mmul_2571

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132792	1 retrocopy	retro_hsap_4819,
Gorilla gorilla	ENSGGOG00000000614	1 retrocopy	retro_ggor_3003,
Macropus eugenii	ENSMEUG00000013001	1 retrocopy	retro_meug_910,
Myotis lucifugus	ENSMLUG00000015803	1 retrocopy	retro_mluc_177,
Macaca mulatta	ENSMMUG00000017224	1 retrocopy	retro_mmul_2571,
Nomascus leucogenys	ENSNLEG00000006291	1 retrocopy	retro_nleu_2194,
Pongo abelii	ENSPPYG00000010989	1 retrocopy	retro_pabe_3747,
Pan troglodytes	ENSPTRG00000023688	1 retrocopy	retro_ptro_3208 ,