RetrogeneDB ID: retro_pabe_2603

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4_random:15236808..15238258(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTN4
• Ensembl ID: ENSPPYG00000009939
• Aliases: None
• Description: alpha-actinin-4 [Source:RefSeq peptide;Acc:NP_001127286]

Sequence

>retro_pabe_2603
GCCTGGGTCCCAGGGAAGGAAGCCATGCTGGAGCACCGGGACTACGAGACCGCCACGCTGTCGGGCATCAAAGCCCTCAT
TCGCAAGCACGAGGCCTTCGAGAGCGACCTGGCTGAGCACCAGGACCGCGTGGAGCAGATCGCAGCCATTGCCCAGGACC
TCAACGAGCTGCATTACTACGACTCCCACAATGTCAACACCCGGGGCCAGAAGATCTGGGACCAGTGGGACGCCCTCAGC
TCTCTGACCAACAGTCGCAAAGAAGCCCTGGAGAAAACAGAGAAGCAGCTGGAGGCCATAGACCAGCTGCACCTGGAGTA
CGCCAAGCACATGGCCCCCTTCAACAACTGGATGGAGAGCGCCATGGAGGACCTCCAGGACATGCTCATCGTGCACACCA
TCGAGGAGATTGAGGGCCTGATCTCAGTCCACGACCAGTTGAAGTCCACCCTGCTGGACACCGACAGCCAGCGCAAGGCC
ATCCTGGCCATCCACAAGGAGGCCCAGAGGATCGCTGAGCGCAACCACATCAAGCTGTGGGGCAGCAACCCCTACACCAC
CCTCACCCCACAGATCATCAACTCCAAGTGGGGGAAGGTGCAGCAGCTGGTGCCAAAACGGGACCACGCCCTCCTGGAGG
AGCAGAGCAAGCAGCAGTCCAACGAGCACCTGCGCCACCAGTTTGCCAGCCAGGCCAACGTCGTGGGGCCCTGGATCCAG
ACCAAGATGGAGGAGATCGGGCGCATCTCCACTGAGATGAACGGGACCCTGGAGGACCAGCTGAGCCACCTGAAGCAGTG
TGAACGCAGCATCGTGGACTACAAGCCCAACCTGGACCTGCTCGAGCAGCAGCACCAGCTTATCCAGGAGGCCCTCATCT
TCGACAACAAGCACACCATGGAGCACATCCGCATGGGTGGGGAGCAGCTGCTCACCACCATTGATTGCCCCAACCATCAA
CGAGGTGGCGAACCAGATCCTCACCCGCAACGCCAAAGGCATCAGCCAGGAGCAGATGCAGGAGTTCCGGGCGTCCTTCA
ACCACTTCGACAAGGATCATGGTGGGGTGCTTGGGCCTGAGGGGTTCAAGGCCTGCCTCATCAGCCTGGGCTATGACGTG
GAGAACGACCGCAGGGTGAGGCCTAGTTTAACCGCATCATGAGCCTGGTCGATCCCAACCACAGCGGCCTTGTGACCTTC
CAAGACTTCATCGACTTCATGTCGCGGGAGACCACCGACACGGACACGGCCGACCAGGTCATCGCCTCCTTCAAGGTCCT
GGCAGGGGACAAGAACTTCATCACAGCTGAGGAGCTGCGGAGAGAGCTGCCCCCCGAACCAGGCTGAGTGCTGTATCGCC
CGCATGGTGCCCTACCAGGGCCCTGACGCCGTGCCCGGTGCCCTCGACTACAAGTCCTCCTCCACGGCCCTGTATGGCGA
GAGCGACCTG

Alignment

ORF - retro_pabe_2603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.16 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AWTDGKEAMLKHRDYETATLSDIKALIRKHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTRCQ
          AW..GKEAML.HRDYETATLS.IKALIRKHEAFESDLA.HQDRVEQIAAIAQ.LNEL.YYDSHNVNTR.Q
Retrocopy AWVPGKEAMLEHRDYETATLSGIKALIRKHEAFESDLAEHQDRVEQIAAIAQDLNELHYYDSHNVNTRGQ

Parental  KICDQWDALGSLTHSRREALEKTEKQLEAIDQLHLEYAKRAAPFNNWMESAMEDLQDMFIVHTIEEIEGL
          KI.DQWDAL.SLT.SR.EALEKTEKQLEAIDQLHLEYAK..APFNNWMESAMEDLQDM.IVHTIEEIEGL
Retrocopy KIWDQWDALSSLTNSRKEALEKTEKQLEAIDQLHLEYAKHMAPFNNWMESAMEDLQDMLIVHTIEEIEGL

Parental  ISAHDQFKSTLPDADREREAILAIHKEAQRIAESNHIKLSGSNPYTTVTPQIINSKWEKVQQLVPKRDHA
          IS.HDQ.KSTL.D.D..R.AILAIHKEAQRIAE.NHIKL.GSNPYTT.TPQIINSKW.KVQQLVPKRDHA
Retrocopy ISVHDQLKSTLLDTDSQRKAILAIHKEAQRIAERNHIKLWGSNPYTTLTPQIINSKWGKVQQLVPKRDHA

Parental  LLEEQSKQQSNEHLRRQFASQANVVGPWIQTKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDL
          LLEEQSKQQSNEHLR.QFASQANVVGPWIQTKMEEIGRIS.EMNGTLEDQLSHLKQ.ERSIVDYKPNLDL
Retrocopy LLEEQSKQQSNEHLRHQFASQANVVGPWIQTKMEEIGRISTEMNGTLEDQLSHLKQCERSIVDYKPNLDL

Parental  LEQQHQLIQEALIFDNKHTNYTMEHIRV-GWEQLLTT-IARTINEVENQILTRDAKGISQEQMQEFRASF
          LEQQHQLIQEALIFDNKH...TMEHIR..G...L.T..IA.TINEV.NQILTR.AKGISQEQMQEFRASF
Retrocopy LEQQHQLIQEALIFDNKH---TMEHIRMGGEQLLTTI>IAPTINEVANQILTRNAKGISQEQMQEFRASF

Parental  NHFDKDHGGALGPEEFKACLISLGYDVENDR-QGEAEFNRIMSLVDPNHSGLVTFQAFIDFMSRETTDTD
          NHFDKDHGG.LGPE.FKACLISLGYDVENDR.QGEA.FNRIMSLVDPNHSGLVTFQ.FIDFMSRETTDTD
Retrocopy NHFDKDHGGVLGPEGFKACLISLGYDVENDR<QGEA*FNRIMSLVDPNHSGLVTFQDFIDFMSRETTDTD

Parental  TADQVIASFKVLAGDKNFITAEELRRELPPD-QAEYCIARMAPYQGPDAVPGALDYKSFSTALYGESDL
          TADQVIASFKVLAGDKNFITAEELRRELPP..QAE.CIARM.PYQGPDAVPGALDYKS.STALYGESDL
Retrocopy TADQVIASFKVLAGDKNFITAEELRRELPPE>QAECCIARMVPYQGPDAVPGALDYKSSSTALYGESDL

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	117.60 RPM
SRP007412_cerebellum	0.00 RPM	65.42 RPM
SRP007412_heart	0.03 RPM	56.02 RPM
SRP007412_kidney	0.00 RPM	237.70 RPM
SRP007412_liver	0.03 RPM	93.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2603 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2603 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130402	1 retrocopy	retro_hsap_2975,
Pongo abelii	ENSPPYG00000009939	1 retrocopy	retro_pabe_2603 ,