RetrogeneDB ID: retro_sscr_62

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:56067054..56068563(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000008335
• Aliases: None
• Description: None

Sequence

>retro_sscr_62
ATGGGGCTCTTGAACAGTCGAATCCTGCGATGCAGGGAGTCAGACACAGCTGAACCACAGCAGCTAGAAGCCCAGGCAGG
CCCCAGTTATGTGTTTGGCAGCCGCAAGCGCAAAGAGAAGAGCGGGCCTTGCTTGGGTCCTGAATCTGAAAACAACTACG
GGTTTCTAGACCAGGAGGATGATCTACAGAAAGTTGTCAGTACAAGCCAGGGTAAAAAAGTTAAGATCGCATCCGAGTAT
GCTTACCAAACTTTATTTTTGAATGGGGAAAATAGTGACATTAAAATCCGTGCTCTTGGGAAAGTATGGTGTTTACACAA
AATGTTTTTATGTCAGTTGGACTATTTTGATACTATATTTAGAGGTTCTTGGAAAGAATCTCCCAAAGATATTATTGATC
TGGAGATTAATGACCAGTATATAAATGTAGAATCCCTGCACTTTGTACTAGGCTCATTGTACAAGGATGAATGCGTCTCA
ATGGAGCCCCTTCAAGTTCCAGGAGTTTTGGCAACTGCATGCCTGCTTCAAGTAGAAGACTTAATTCAGCAATGTAATGA
GACTATGAAGGAAACAATTAATGTGAAAACTGTATGTGGCTATTATGCAGCAGCAGAGACCTATGGGTTAGATTCTGTAA
AGACAGGGTGCTTTGAATGGCTTCTCCACAATTTGATGACTCACCCAAGTGTTGAACTTTACAAAGACCTCAGTACAGAT
CTTATGAATTTGCTCATTTCTTCTTCTAATTTATTAGTAATGCAAAAAGAAATGGATGTATACACCACACTTAAAGAGTG
GATGTTCCTCCGCCTTAACCCTGCTTGGAACGGCTCAATGAAACAGCTTTTAGTTAATGCAAACAACTGGTTTTCCAGGC
ACAGGGAAGGTGTTGGTAACACTGCCTTTCTTGAAACCAATCAAGGCATAGTATTTCAACCAGTATTTAAAAATTTGAGG
TTTCAACATATAATCTGCGACCTGGCCTCCGCAAGAGTTATTGAACAAGATGCGCTAATACCTTCAAAATGGCTATCATC
TGTTTATAAACAGCAGTGGTTTACCTTGCTTAGAGCACAACAATTCAGTGAAATTGGGCCTAGAGACATTAATGAAACAG
AACTTGAAGAATATAGCATGAGATGTGGCAAAAGGATTGTCAAGGATGGAAAGTATTCTTGGAAGTGGTCAGGTTATAAC
TTTGGCTTTCCTTTACATGTCATCTTCACCAGCCATTATATAATTTTCAAACAGAATACTTTCAGTCAGCCATATGATGG
TTCCACCTGTTTACAGAATCTAAGAAATATTGCATTCAGATTAACTTTGGTATATTTCGATTCTAGTGGAAAATTGAGTT
TCAGAAAAACAACTGGTTATAAAATTCTTACCTTTGAAAGGGATGAGGAACAAGTGGTAATGAAGTTGGATAGCATAGCT
CTCAGCTTCCCTTTATATATATTCTGTAACTTCCTGTTTATATCATTAGAAAATCCAGGAAATCGGTAA

Alignment

ORF - retro_sscr_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 87.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKRSSGAFCYCHPDSETDEDE-EEGDEQQRLLNTPRSRKKLKSTSKYIYQTLFLNGENSDIKICALGEEW
          RKR.........P.SE.........D..Q....T....KK.K..S.Y.YQTLFLNGENSDIKI.ALG..W
Retrocopy RKRKEKSGPCLGPESENNYGFLDQEDDLQKVVSTSQG-KKVKIASEYAYQTLFLNGENSDIKIRALGKVW

Parental  SLHKIYLCQSGYFSSMFSGSWKESSMNTIELEIPDQNIDIEALQVAFGSLYRDD-VLIKPSRVIAILAAA
          .LHK..LCQ..YF...F.GSWKES....I.LEI.DQ.I..E.L....GSLY.D..V...P..V...LA.A
Retrocopy CLHKMFLCQLDYFDTIFRGSWKESPKDIIDLEINDQYINVESLHFVLGSLYKDECVSMEPLQVPGVLATA

Parental  CMLQLDGLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVMK
          C.LQ...LIQQC.ETMKETINVKTVCGYY..A.TYGLDSVK..C.EWLL.NLMTH..VEL.K.LS...M.
Retrocopy CLLQVEDLIQQCNETMKETINVKTVCGYYAAAETYGLDSVKTGCFEWLLHNLMTHPSVELYKDLSTDLMN

Parental  QLIGSSNLFVMQVEMDVYTALVSKWMFLQLVPSWNGSLKQLLTETDVWFSKRKKDFEGMTFLETEQGKPF
          .LI.SSNL.VMQ.EMDVYT.L...WMFL.L.P.WNGS.KQLL.....WFS..........FLET.QG..F
Retrocopy LLISSSNLLVMQKEMDVYTTL-KEWMFLRLNPAWNGSMKQLLVNANNWFSRHREGVGNTAFLETNQGIVF

Parental  VSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSAVYKQQWLAMLRAEQDSEVGPQEINKEELEGNSMRC
          ..VF..LR.Q.II.DLASAR.IEQD.L.PS.WLS.VYKQQW...LRA.Q.SE.GP..IN..ELE..SMRC
Retrocopy QPVFKNLRFQHIICDLASARVIEQDALIPSKWLSSVYKQQWFTLLRAQQFSEIGPRDINETELEEYSMRC

Parental  GRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKL
          G....KDG.Y.W.W.G.NFGF.L.V..T..YIIFK.NT..QP..GS..LQ..R.IAFRL.L..FDSSGKL
Retrocopy GKRIVKDGKYSWKWSGYNFGFPLHVIFTSHYIIFKQNTFSQPYDGSTCLQNLRNIAFRLTLVYFDSSGKL

Parental  ICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYISPE
          ....TTGY.ILT.E.D.EQVVM.LDS..L.FPLYI.CNFL.IS.E
Retrocopy SFRKTTGYKILTFERDEEQVVMKLDSIALSFPLYIFCNFLFISLE

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	0.00 RPM	4.11 RPM
SRP014902_testis	0.28 RPM	12.16 RPM
SRP018288_heart	0.03 RPM	5.50 RPM
SRP018288_kidney	0.00 RPM	25.91 RPM
SRP018288_liver	0.00 RPM	14.55 RPM
SRP018288_lung	0.00 RPM	23.32 RPM
SRP018856_adipose	0.00 RPM	6.65 RPM
SRP035408_brain	0.00 RPM	2.92 RPM
SRP035408_liver	0.00 RPM	8.16 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_62 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_62 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62 ,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,