RetrogeneDB ID: retro_sscr_901

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:54419619..54420479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000021742
• Aliases: None
• Description: None

Sequence

>retro_sscr_901
AAAGTACCTGCCATCTGGGTAGAAGATGAACCGCTTCTGAGAAAAAACCACAGCTGTGCACCATCTTCCCCATCAAATAC
CACGGTATTCTGGCAGGTATACCAGCAGGCCGATGATAATTGTTCCTCTCATGCAGCTGAGGGGCTAGGTCTCTCCAAGG
ACATTTAGCATCAGAAACCTGGAAGCCGTGGAGAGAGATTTTTGTATCCATTTCTGACTCTCATTGTCGAAAGTGATGAT
GGAGCTGGAGCTTAAAATGTGGTGTGGTGATTTAGACCAAAAGTGCGGATTACAGAAGTGTGATGTTTCGATGGCTCTCC
ATGTGACACAGACCACATGCATTCTGAAATGCAGAGTTTCCTTATCAACACTTGCATTAAAGGTTGCAGAGAGGAGGCTT
TTCTCCTCCAGGCCATTGAGATGCTGCCCTGTATAAAGAAGAAGGCTCTCTGGGCCTGGCTGGGGACAAGGAAGTTGCTC
GTGGAGAAGGGGCTGTCCCTTGGTGCCAATGGAGGAAAGCTCTTTTGGAGCCTCTGTGTCAACATTCTGCCTTAAGAAAT
GAGAATCGATGCCCGAGATCACATTTTCCGGTGAATTTCCTTGCAGAGATGAGGTTTACACAAGTGACTTTGCTTGCCTC
ATATTTAAACACTTGTTACACAAACCTTCAGAGTAAAAAGTAAAAGAAATAACTACCAGGGCTATGAAGATGGAATAAGA
GTTCCTAACTGAGACCTTGCCTTGAGGTTTATTGGAATGAGCTGTGCTCTGATGAGGCAGTACCTGGCATTTGTAGCAGA
CAGACTTATGCTAGATCTGGGTTTTAGGACAGTTTCAGAGCAGAAAATCCATTTGACTTC

Alignment

ORF - retro_sscr_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.84 %
• Parental protein coverage: 87.84 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KLSAPSVEDEPLLREN-PRRFVIFPIEYHDI-WQMYKKAE--ASFWTAEEVDLSKDIQHWETLKPEERYF
          K..A..VEDEPLLR.N.P....IFPI.YH.I.WQ.Y..A....S...AE...LSKDI.H.......ER..
Retrocopy KVPAIWVEDEPLLRKN<PQLCTIFPIKYHGI>WQVYQQADDNCSSHAAEGLGLSKDI*HQKPGSRGERFL

Parental  ISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREFLFNA
          ...........DG....N.V..F...V.ITE..CF.G........HSEM.S.LI.T.IK...E..FL..A
Retrocopy YPFLTLIVESDDGAGA*NVVW*FRPKVRITEV*CFDGSPCDTDHMHSEMQSFLINTCIKGCREEAFLLQA

Parental  IETMPCVKKKADWALRWI-GDKEATYGERVVAF-AAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISR
          IE..PC.KKKA.WA..W..GDKE...GE..V......E...F..S..S.F.LKK...MP..TFS.E...R
Retrocopy IEMLPCIKKKALWA--WL<GDKEVARGEGAVPW<VPMEESSFGAS-VSTFCLKK*ESMPEITFSGEFPCR

Parental  DEGLHCDFACLMFKHLLHKPSEQRVKEIIVNAVRIEQEFLTEALP-VKLIGMNCTLMKQYIEFVADRLML
          DE....DFACL.FKHLLHKPSE..VKEI...A...E.EFLTE.LP....IGM.C.LM.QY..FVADRLML
Retrocopy DEVYTSDFACLIFKHLLHKPSE*KVKEITTRAMKME*EFLTETLP<LRFIGMSCALMRQYLAFVADRLML

Parental  ELGFGKV-FRVENPFDF
          .LGF..V.FR.ENPFDF
Retrocopy DLGFRTV<FRAENPFDF

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	3.98 RPM
SRP014902_testis	0.00 RPM	12.87 RPM
SRP018288_heart	0.00 RPM	4.37 RPM
SRP018288_kidney	0.00 RPM	6.11 RPM
SRP018288_liver	0.00 RPM	7.36 RPM
SRP018288_lung	0.41 RPM	16.19 RPM
SRP018856_adipose	0.00 RPM	1.14 RPM
SRP035408_brain	0.00 RPM	2.89 RPM
SRP035408_liver	0.00 RPM	43.36 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_901 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_901 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901 ,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,