RetrogeneDB ID: retro_pabe_3475

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:55970806..55971723(-)
• Located in intron of: ENSPPYG00000019222

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSPPYG00000008735
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_pabe_3475
TTAACCAACTGGGACAACATGGAGAAGATCTGGCAGCACAACCTTTCTACAGGAGGAGCTGCGTGTGGCTCCCGAGGAGC
ACCCCATGCTGCTGACCGAGGCCCCCCCTGAACCCCAAGGGCCAGCCCGCGAGAAGATGACCCGAATGATGTTTGAGACC
TTTTAACACCCCAGCCATGGTACATGGCCATCCAGCCCGTGCTGTCCCTGTACTTCTCTGGCTGTACCACTGGTATTGTG
ATGGACTCCGGTGACGGGGTCACCCACAGTGTACCCATCTATGAGGGGTATGCTCTCCCCCACACCATCCTGTGTCTGGA
CCTGGCTGGCCGGGACCTGACTGACTACCTCATGGAGATCCTTACTGAGCGCGGCTACAGCTTCACCACCACGGCTGAGT
GGGATATCGTGCGTGACATCAAGGAGAAGCTGTGCTATGTCACTCTGGGCCTTCGAGCAGGAGATGGGCCATGGCGGCNC
TCCAGCTCCCTCCCTGGGAGAAGAGCCTACGAGCTGCCTGACGGCCAGGTCATCACCNTCGGCAATGAGCAATTCTGCTG
CCCTGAGGCACTCTTCCAGCTTTCCTTCCTGGGCATAGAATCCTGTGGCATCCATGAAACTACCTTCAACTCCGTTATGA
AGTGTGACGTGGGACATCCCACAATAGACGTTTATGCCAACCCATTGTTGTCTGGCGGCACCACCATGTACCCTAGCATT
GCCAACAGGATGCAGAAGGAGATCACCTCCCTGGCGCCCAGCACGATGAAGATCAAGATCATTGCTTCTCCCGAGCTCAA
GCACTCTGTGTGGATTGGCGGCTCCATCCTGGCCTCGCTGTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATG
ATGAGTCCGGCTCCATCATCCTTCCTTCAAATGCTTC

Alignment

ORF - retro_pabe_3475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 80.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VTNWDDMEKIWHH-TFYNE-LRVAPEEHPVLLTEAPLNPKAN-REKMTQIMFETF-NTPAM-YVAIQAVL
          .TNWD.MEKIW.H.TF..E.LRVAPEEHP.LLTEAP..P....REKMT..MFETF.NTPAM.Y.AIQ.VL
Retrocopy LTNWDNMEKIWQH>TFLQEELRVAPEEHPMLLTEAPPEPQGPAREKMTRMMFETF>NTPAM>YMAIQPVL

Parental  SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLY.SG.TTGIVMDSGDGVTH.VPIYEGYALPH.IL.LDLAGRDLTDYLM.ILTERGYSFTTTAE..IVR
Retrocopy SLYFSGCTTGIVMDSGDGVTHSVPIYEGYALPHTILCLDLAGRDLTDYLMEILTERGYSFTTTAEWDIVR

Parental  DIKEKLCYVALD-FEQEMATAA-SSSSL--EKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHE
          DIKEKLCYV.L..FEQEM......SSSL.....YELPDGQVIT.GNE.F.CPEALFQ.SFLG.ESCGIHE
Retrocopy DIKEKLCYVTLG>FEQEMGHGG<XSSSLPGRRAYELPDGQVITXGNEQFCCPEALFQLSFLGIESCGIHE

Parental  TTFNSIMKCDVDIRK-DLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSI
          TTFNS.MKCDV.....D.YAN..LSGGTTMYP.IA.RMQKEIT.LAPSTMKIKIIA.PE.K.SVWIGGSI
Retrocopy TTFNSVMKCDVGHPTIDVYANPLLSGGTTMYPSIANRMQKEITSLAPSTMKIKIIASPELKHSVWIGGSI

Parental  LASLSTFQQMWISKQEYDESGPSIVHR-KCF
          LASLSTFQQMWISKQEYDESG..I....KCF
Retrocopy LASLSTFQQMWISKQEYDESGSIILPS<KCF

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	426.62 RPM
SRP007412_cerebellum	0.36 RPM	117.22 RPM
SRP007412_heart	0.03 RPM	145.94 RPM
SRP007412_kidney	0.10 RPM	354.54 RPM
SRP007412_liver	0.21 RPM	440.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3475 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3475 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2805
Gorilla gorilla	retro_ggor_2774

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
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,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,