RetrogeneDB ID: retro_sscr_540

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:23318625..23319417(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSSSCG00000022912
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_sscr_540
GTGAAAATGATTCCAGAATTCCAAAGTTCAGTTTGCATCAACCCTCACAAGATTAGAAGAAATTATCTGTGGTCTTAACA
AAGGAGGAGCTGCCAAACTTCGGATAATAACAGACTTCGATATGACACTGAGTCAATTTTCCTACAGAGGGAAAAGATGC
CCATTATGTCATAATGTCATTGACAACTGTAAGCTAATTACAGATGAATGTCAAGAAAAGTTACTGCAGCTAAAGGAAGA
GTATTATACTATTGAAATGGATCCTGTTCTTTACTGTAAAAGAGCAGTATCCTTACATAGTAGAATGGTATAATAAATCA
CATGGTTTGCTTGCTGAACAGGCTTTACCAAAAGCCAAACTTACAGAAATTATGGAAGAATCTAACGTTATGCTCAAGGA
AGGGTATGAGAATTTATATGATAAGCTCTGACAATACAGCATCTCTGTGTTCATATTTTCAGCTGGTACTGGTAATATAC
TAGAGGAGGTTATTTGTCAAGCTGCTGTTTATTATCCAAACGTCGAAGTAGTATCCAACGTCATGGATTTTTATTACAAT
GGGCTGCTCAAAGGATTTAAAGGAGAACCAATTCATGTGTTTAACAAACATGATGGTTCCTTGAAGAATACAGAATATTT
CAATCAATTGAAAAAACAATAGCAACATAATTCTGGCAGACTCCTGAGGGGACTTATAAATGGCATGTGGAGTAACCAAT
GTTGAACACATTCTGAAAACTGGATATCTAAATGATAGAGTGGATGAGCTTTTAGGAAAGTACATGGACTCA

Alignment

ORF - retro_sscr_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 79.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IEMMPEFQKSSVRIKNP-TKVEEIICGLIKGGAAKLQVITDFDMTLSRFSYRGKRCPSCHNVIDNCKLIT
          ..M.PEFQ.SSV.I.NP.T..EEIICGL.KGGAAKL..ITDFDMTLS.FSYRGKRCP.CHNVIDNCKLIT
Retrocopy VKMIPEFQ-SSVCI-NP>TRLEEIICGLNKGGAAKLRIITDFDMTLSQFSYRGKRCPLCHNVIDNCKLIT

Parental  DECREKLLQLKEKYYAIEIDPVL-TVEEKYPYIVEWYTKSHGLLIEQALPKAKLKEIVEESDIMLKEGYE
          DEC.EKLLQLKE.YY.IE.DPVL.TV.E.YPYIVEWY.KSHGLL.EQALPKAKL.EI.EES..MLKEGYE
Retrocopy DECQEKLLQLKEEYYTIEMDPVL>TVKEQYPYIVEWYNKSHGLLAEQALPKAKLTEIMEESNVMLKEGYE

Parental  NFFDKLQQYNIPVFIFSAGIGDVLEEVIRQAGVYYPNVKVVSNFMDFDDNGLLRGFKGELIHVFNKHDGS
          N..DKL.QY.I.VFIFSAG.G..LEEVI.QA.VYYPNV.VVSN.MDF..NGLL.GFKGE.IHVFNKHDGS
Retrocopy NLYDKL*QYSISVFIFSAGTGNILEEVICQAAVYYPNVEVVSNVMDFYYNGLLKGFKGEPIHVFNKHDGS

Parental  LKNTEYFNQLK-NNSNIILLGDSQGDLKMADGVANVEHILKIGYLNDRVDELLEKYMDS
          LKNTEYFNQLK.NNSNII.L.DS.GDL.MA.GV.NVEHILK.GYLNDRVDELL.KYMDS
Retrocopy LKNTEYFNQLK>NNSNII-LADS*GDL*MACGVTNVEHILKTGYLNDRVDELLGKYMDS

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	2.52 RPM
SRP014902_testis	0.00 RPM	10.33 RPM
SRP018288_heart	0.03 RPM	12.36 RPM
SRP018288_kidney	0.00 RPM	19.80 RPM
SRP018288_liver	0.00 RPM	41.90 RPM
SRP018288_lung	0.10 RPM	12.42 RPM
SRP018856_adipose	0.00 RPM	5.68 RPM
SRP035408_brain	0.00 RPM	15.53 RPM
SRP035408_liver	0.00 RPM	54.48 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_540 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540 ,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,