RetrogeneDB ID: retro_sscr_389

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:154028167..154029258(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BETA-ACTIN
• Ensembl ID: ENSSSCG00000028355
• Aliases: None
• Description: Actin, cytoplasmic 1 [Source:UniProtKB/TrEMBL;Acc:I3LVD5]

Sequence

>retro_sscr_389
CTCATCATCGACAGTGACTCTGGCATGTGCAACGCTGGCTTTGCTGGGGTGACGCCCCTGGGGCTGTGTTCCCATCCATC
ACTGGGCATCCCCGAAACCAGGGCATCATGGGGCATGGGGCAGAAGGACAGCTATGTGCATGACAAGGCCCAGAACAATC
ATGGCATCCTGACCCTCAAGTACTCCACTGAGCCCAGCATTGTCACCAACTGGGATGACATGGAGAAGATCTGGCACCAC
ACCTACAATGAGCTGCGTGTGGCCCCTGAGGAGCACCTTGTGCTAACGACAAAGGCCCCCTGAACTCCAAGGACAACTGT
GAGACGATAACTCAGTTCATGTTGGAGATTTTCAACACTCCAGCCATATGTGTGGCCATCCAGGCCATTGCTGTCCCTGT
ACACCTCTGGCTGCACTTGCACTGTCATGGACTCTGGGGACAGGGTTACCCACATGGTGCCCATCTATGAAGGGTATGGC
CTGTCTCAGGCTATCCTGCATCTGGACCTGGCTGGCCGAGTCCTGACCCACTACTTCATAAAGATCCTCATGGACCGGGG
CTGAAGGTTCACCACCACAGAGGAGTGGGAGATCATGGGTGACATCAAGGAGAAACTCTGCTGTGTCACCCTGGACTTCA
AGCAGGAGATAGCCACCACCATGTCCTCCTCCTCCATGGAGAAAAGCTACAGGCTTCCCGAAGACCAGGTGATCACCATA
AGCAACAAGTGGTTCAGGTGTCCAGACATGCTCTTCCAGTCCTCTTTCCTGGGTATGGAGTTCTGTGGCATCCACAAGAC
CACCTTCAACTGCATCATGAAGTGTGACAGCGACATCAAGAAGGGCCTGTATGCCAACACAGTGCTGTCTGGTGGGACCA
CCATGTACCCTGGCATCCCCAACAGGACGCAGGAGATCACAGCTCTGGTCCCCACCATGATGAAGATCAAGATCATGGCT
CCTCCCTAGTGCATGTACTCTGCGTGGATCGGGGGTTCCACCCTGGCCTCACTATCTGCCTTCCAGCAGATGTGATCAGC
CAGCAGGAGTGGGACAATTCAGGCCAGTCCATCATCCACCACAAATACTTC

Alignment

ORF - retro_sscr_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LVIDNGSGMCKAGFAG-DDAPRAVFPSIVGRPRHQGVMVGMG-QKDSYVGDEAQSKRGILTLKYPIEHGI
          L.ID..SGMC.AGFAG..DAP.AVFPSI.G.PR.QG.M.G.G.QKDSYV.D.AQ...GILTLKY..E..I
Retrocopy LIIDSDSGMCNAGFAG<GDAPGAVFPSITGHPRNQGIM-GHG>QKDSYVHDKAQNNHGILTLKYSTEPSI

Parental  VTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEA-PLNPKANREKMTQIMFETFNTPAMYVAIQAV-LSLY
          VTNWDDMEKIWHHT.YNELRVAPEEH.VL.T.A.PLN.K.N.E..TQ.M.E.FNTPA..VAIQA..LSLY
Retrocopy VTNWDDMEKIWHHT-YNELRVAPEEHLVLTTKA<PLNSKDNCETITQFMLEIFNTPAICVAIQAI>LSLY

Parental  ASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIK
          .SG..T..VMDSGD.VTH.VPIYEGY.L..AIL.LDLAGR.LT.Y..KIL..RG..FTTT.E.EI..DIK
Retrocopy TSG-CTCTVMDSGDRVTHMVPIYEGYGLSQAILHLDLAGRVLTHYFIKILMDRG*RFTTTEEWEIMGDIK

Parental  EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIM
          EKLC.V.LDF.QE.AT..SSSS.EKSY.LP..QVITI.N..FRCP..LFQ.SFLGME.CGIH.TTFN.IM
Retrocopy EKLCCVTLDFKQEIATTMSSSSMEKSYRLPEDQVITISNKWFRCPDMLFQSSFLGMEFCGIHKTTFNCIM

Parental  KCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQ
          KCD.DI.K.LYANTVLSGGTTMYPGI..R.Q.EITAL.P..MKIKI.APP...YS.WIGGS.LASLS.FQ
Retrocopy KCDSDIKKGLYANTVLSGGTTMYPGIPNRTQ-EITALVPTMMKIKIMAPP*CMYSAWIGGSTLASLSAFQ

Parental  QM-WISKQEYDESGPSIVHRKCF
          QM..IS.QE.D.SG.SI.H.K.F
Retrocopy QM<VISQQEWDNSGQSIIHHKYF

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
SRP014902_placenta	0.40 RPM	11200.10 RPM
SRP014902_testis	1.27 RPM	1628.33 RPM
SRP018288_heart	0.29 RPM	302.35 RPM
SRP018288_kidney	0.00 RPM	1004.46 RPM
SRP018288_liver	0.00 RPM	379.15 RPM
SRP018288_lung	0.10 RPM	2518.06 RPM
SRP018856_adipose	0.28 RPM	1581.09 RPM
SRP035408_brain	0.00 RPM	2276.49 RPM
SRP035408_liver	0.06 RPM	518.89 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_389 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 63 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	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,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
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,