RetrogeneDB ID: retro_pabe_1317

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:80162096..80162895(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000006732
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTC1
• Ensembl ID: ENSPPYG00000006318
• Aliases: None
• Description: actin, alpha, cardiac muscle 1 [Source:HGNC Symbol;Acc:143]

Sequence

>retro_pabe_1317
CCCCTGAGCCCCAAGGCCAACAGAGAGAAGATGATTCAGATCATGTTTGGGGCCTTCAACACCCCAGTCAACTACAGGGC
CATTCAGGTCACCCTGTCCCTGCATGCCTCTGTCAGTGCCATTGGCACCATGGGGGACTCAGGTGATGGGGTCACCCACA
CTTGCCCATCTCCAAGGATACCGCCACCCTCCCCCAGTCATCCTGTGTTTGGCCCTGGCTGGCCGGGACCTGGCCGGCTA
CGTGGTGAAGATCCTCGTGGGGCCTGCTACAGCTTAATCACCACAGTGAACTGGGGGATTGTGCGTGACATCCAGGAAAA
GCTGTGCTGTGTTGCCTTGGACTTGCAGCAGGAGATCCCACTGCCGTGTCCTCTTCCTTCCTGGAGAAGAGCTACGAGCT
GTCCCACAGCCTGGTGGTCACCATCAGCAATGAGTGGTTCTGGTGTCCAGAGGCGCTGTCTCAGCCCTCCTTCCTGGGCA
TGGAATCTTGCTGCATCCAGGAGACCACCTTGAGCTCCATCATGAAGTGTGATGTGGATATCTGCAAGGACCTGTACACC
AATGTGGTGCTGTCTGGCAGCATTGCCATGCACCCAAGCGTCACACACAGGATGTAGAAGGAGATCACTGCCCCGGCACC
AGGACCATGAAGATCAAGATCATGGCTGTCTCTGAGCACAAGTATTCCATGTGGATCAGCAGCTCCATCCTGGCCTCACT
GTCCACCTTCCAGCCAATGTGGATCAGCAAGCGGGGGTGCCACCAGTCAGGCCCCTCCACTGTTCACCGCAAATGCTTC

Alignment

ORF - retro_pabe_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 70.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTH-NVPI-YEGYALPH-AI
          PL.PKANREKM.QIMF..FN.P..Y.AIQ..LSL.AS....G...DSGDGVTH...PI...GY..P...I
Retrocopy PLSPKANREKMIQIMFGAFNTPVNYRAIQVTLSLHASVSAIGTMGDSGDGVTH<HLPI<LQGYRHPPPVI

Parental  MRLDLAGRDLTDYLMKILTERG-YSFVTTAEREIVRDIKEKLCYVALDFENEMA-TAASSSSLEKSYELP
          ..L.LAGRDL..Y..KIL.....YS..TT....IVRDI.EKLC.VALD...E...TA.SSS.LEKSYEL.
Retrocopy LCLALAGRDLAGYVVKILVGPA<YSLITTVNWGIVRDIQEKLCCVALDLQQEIP<TAVSSSFLEKSYELS

Parental  DGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRM
          ...V.TI.NE.F.CPE.L.QPSF.GMES..I.ETT..SIMKCD.DI.KDLY.N.VLSG...M.P....RM
Retrocopy HSLVVTISNEWFWCPEALSQPSFLGMESCCIQETTLSSIMKCDVDICKDLYTNVVLSGSIAMHPSVTHRM

Parental  QKEITALAPS-TMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDEAGPSIVHRKCF
          .KEITA.AP..TMKIKI.A..E.KYS.WI..SILASLSTFQ.MWISK......GPS.VHRKCF
Retrocopy *KEITAPAPG<TMKIKIMAVSEHKYSMWISSSILASLSTFQPMWISKRGCHQSGPSTVHRKCF

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	0.22 RPM	17.31 RPM
SRP007412_cerebellum	0.12 RPM	1.46 RPM
SRP007412_heart	0.12 RPM	3683.43 RPM
SRP007412_kidney	0.36 RPM	0.56 RPM
SRP007412_liver	0.21 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1317 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000011801	1 retrocopy	retro_lcha_19,
Oryctolagus cuniculus	ENSOCUG00000004074	1 retrocopy	retro_ocun_38,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Pongo abelii	ENSPPYG00000002605	1 retrocopy	retro_pabe_1930,
Pongo abelii	ENSPPYG00000006318	1 retrocopy	retro_pabe_1317 ,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,