RetrogeneDB ID: retro_pabe_3747

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:47179123..47180707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNBL1
• Ensembl ID: ENSPPYG00000010989
• Aliases: None
• Description: catenin, beta like 1 [Source:HGNC Symbol;Acc:15879]

Sequence

>retro_pabe_3747
GACATGGGCAAACTTCTGAGCTACCAGCCCAACAGGGGCATAAAACGTCCCCGAGATGACAAAGAGGAGGAGCAGAAGAT
GCATCAGAAACAAACTAGTACTCAAGATTGGGAAGAGGAAATGATTGTGGTGGAAGAAGCAGAGGATGACAAAAAATGGC
TGCTTCAGATTATTGACACAGAGAGTGAGGAGGAAGAGAAAGAGGAGGAGCCATTGGATGAAAGCTCAGTGAAGAAAATG
ATCCTCACATTTGAATAGTGAGCATATAAAAACCAAGAATTGCAGATTAAGTTTCCAGACAATCCAGAGAAGTTCATGAA
ATCCCAACTGGACCTACATGACATCATTCAGAAGATGCACGTGGTGGCCACCATGCCAGACCTGTACCTTTTGCTGGAGC
TGAATGCTGTGCAGTCACTTCTTGGGTTGCTTGGACACAATAATACAGATGTGTCCATAGCTGGGGTTGATTTGAGTCAG
GAATTAAAAGATATAGACATCTTCTATGAGAGTGAAGAGGGAGCAGAATTACTCATTGATGCGCTGGTGGATGGGCAGGT
GATAGCACTGCTGGTGCAGAACGTGGAGCACCTGGATGAGTCTGTGAAGGAGCAGGCCAATGGTGTCCATAACACTCTTG
TTATTGTAGAAAACATGGCTGAGTTCTAGCTGGAGATGTGTACAAAAGGTGCCCAGCAGGGTCTTCCTCAGTGGCTGTTG
AAGAGGCTGAAGGCAAAGAAGCCTTTTGATGCCAACAAACTGTATTGCAGTGAAATGCAGGCCATATTGCTCCAGGACAA
CGATGAAAACAGGAAATTGCTTGGGGAGCTGGATGGAATTGATGCACTTCTTCAGCAGTTATCTGTGTTTAAAAGACAAA
ATCCCAGCACAGCAAAGGAGCAGGAGATGATGGAGAATCTGTTTGATTCACTCTGCTTCTAACTAATGCTCACTTCCAAT
CATGAGCACTTCCTGAAGGGCGAGGGTCTTCAGGTGATGCATCTCATGCTCAGGGAAATGAAGATCTCACGGAGTGGGGT
CCTGAAAGTGCTGATTGCACCCGAGGGCATCTACAACTGCGGTAAATTTGTTGACATTCTTGGCTTATGAACCATCTTTC
CCCTCTTTATGGAATTTCCCAGGAAGATCAAGAAAGTGGGTACCACTGACAAGGAACACAAAGAGCATATCTGTTCCATT
CTGGCTTCCCTTTTGTGGAACCTGAGAGGGCATCAGCGAACCCGGCTTCTGAATAAATTCACTGAAAATGACAGTGAGTA
GGCTGATAGACTAATGGAGTTGCATTTTCAATATCTGGGTGCAATGCAAGTGGCAGACAAGAGGAATGAAGGGGAAAAAC
ATGACATGGTCCAGCGTGGAGAGATCATAGACGGTGACATGGGGGATGAGTTCTACCTCCAGTGCTTGGATGCAGAGCTC
TTTGTTCTCCAGTGCATCTGCTGCATTATGGCCAAGATCTGCAATGCCAATGTCCCCCAGATTTGCCAGAGGGTTCACCA
GATCCTAAACATGTGAGGACGCTCCATCAAAATTGTCAGGCATATCATCAAGGGGTATGCGGAG

Alignment

ORF - retro_pabe_3747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.7 %
• Parental protein coverage: 95.38 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVGELLSYQPNRGTKRPRDDEEEEQKMRRKQTGTRERGRYREEEMTVVEEADDDKKRLLQIIDRDGEEEE
          D.G.LLSYQPNRG.KRPRDD...E......Q..T.......EEEM.VVEEA.DDKK.LLQIID...EEEE
Retrocopy DMGKLLSYQPNRGIKRPRDDK--EEEQKMHQKQTSTQDW--EEEMIVVEEAEDDKKWLLQIIDTESEEEE

Parental  EEEEPLDESSVKKMILTFEKRSYKNQELRIKFPDNPEKFMESELDLNDIIQEMHVVATMPDLYHLLVELN
          .EEEPLDESSVKKMILTFE...YKNQEL.IKFPDNPEKFM.S.LDL.DIIQ.MHVVATMPDLY.LL.ELN
Retrocopy KEEEPLDESSVKKMILTFE**AYKNQELQIKFPDNPEKFMKSQLDLHDIIQKMHVVATMPDLY-LLLELN

Parental  AVQSLLGLLGHDNTDVSIAVVDLLQELTDIDTLHESEEGAEVLIDALVDGQVVALLVQNLERLDESVKEE
          AVQSLLGLLGH.NTDVSIA.VDL.QEL.DID...ESEEGAE.LIDALVDGQV.ALLVQN.E.LDESVKE.
Retrocopy AVQSLLGLLGHNNTDVSIAGVDLSQELKDIDIFYESEEGAELLIDALVDGQVIALLVQNVEHLDESVKEQ

Parental  ADGVHNTLAIVENMAEFRPEMCTEGAQQGLLQWLLKRLKAKMPFDANKLYCSEVLAILLQDNDENRELLG
          A.GVHNTL.IVENMAEF..EMCT.GAQQGL.QWLLKRLKAK.PFDANKLYCSE..AILLQDNDENR.LLG
Retrocopy ANGVHNTLVIVENMAEF*LEMCTKGAQQGLPQWLLKRLKAKKPFDANKLYCSEMQAILLQDNDENRKLLG

Parental  ELDGIDVLLQQLSVFKRHNPSTAEEQEMMENLFDSLCSCLMLSSNRERFLKGEGLQLMNLMLREKKISRS
          ELDGID.LLQQLSVFKR.NPSTA.EQEMMENLFDSLC..LML.SN.E.FLKGEGLQ.M.LMLRE.KISRS
Retrocopy ELDGIDALLQQLSVFKRQNPSTAKEQEMMENLFDSLCF*LMLTSNHEHFLKGEGLQVMHLMLREMKISRS

Parental  SALKVLDHAMIGPEGTDNCHKFVDILGLRTIFPLFMKSPRKIKKVGTTEKEHEEHVCSILASLLRNLRGQ
          ..LKVL....I.PEG..NC.KFVDILGL.TIFPLFM..PRKIKKVGTT.KEH.EH.CSILASLL.NLRG.
Retrocopy GVLKVL----IAPEGIYNCGKFVDILGL*TIFPLFMEFPRKIKKVGTTDKEHKEHICSILASLLWNLRGH

Parental  QRTRLLNKFTENDSEKVDRLMELHFKYLGAMQVADKKIEGEKHDMVRRGEIIDSDTEEEFYLRRLDAGLF
          QRTRLLNKFTENDSE..DRLMELHF.YLGAMQVADK..EGEKHDMV.RGEIID.D...EFYL..LDA.LF
Retrocopy QRTRLLNKFTENDSE*ADRLMELHFQYLGAMQVADKRNEGEKHDMVQRGEIIDGDMGDEFYLQCLDAELF

Parental  VLQHICYIMAEICNANVPQIRQRVHQILNMRGSSIKIVRHIIKEYAE
          VLQ.IC.IMA.ICNANVPQI.QRVHQILNM.G.SIKIVRHIIK.YAE
Retrocopy VLQCICCIMAKICNANVPQICQRVHQILNM*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	23.55 RPM
SRP007412_cerebellum	0.00 RPM	27.12 RPM
SRP007412_heart	0.00 RPM	15.11 RPM
SRP007412_kidney	0.00 RPM	24.16 RPM
SRP007412_liver	0.03 RPM	18.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3747 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3747 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4819
Pan troglodytes	retro_ptro_3208
Gorilla gorilla	retro_ggor_3003
Macaca mulatta	retro_mmul_2571

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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,