RetrogeneDB ID: retro_sscr_23

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:80803504..80804803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000000811
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSSSCG00000007168
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_sscr_23
ATGGTCCACCTGTGGACGGCCGACGTGCAGCAGCTGCTCCACAACAAATTCGTAGTCATCCTGGGGGACTCTGTCCAGCG
GGCTGTGTACAAGGACCTGGTGCTCCTGCTGCAGAAGAATGACCTGCTCACTCTCAGCCAGCTCAAGGCCAAGGGGGAAC
ACAGCTTCGAACAGGATCGGCTGGTCTCCGGAGGCCAGCAGGGCCGCATGCACAACGGCATCCAGTACCGCGAGGTGCGT
CAGTTTTGCTCCGACCACCACCTGGTGCGCTTCTACTTCCTGACACGCGTGTACTCCGACTACCTCGAAGACATCCTGGA
GGAGCTGCAGTCAGGGGAGCACGCCCCGGATTTGGTCATCATGAACTCCTGCCTCTGGGACCTTACCAGGTACGGGGAGG
ACTCCTGGCCGAGCTACCTGCGAAACCTGGAGAGCCTGTTTGGGCGCCTGCACCATGTGCTGCCGGAGTCGTGCCTCTTT
GTATGGAACACGGCCATGCCCGTGGGCGACAACATCACCAGCGGCTTCATTCCACCTGAGCTCCGGGCCACGGCCTCCCT
CCACCTGAAAATCCAGGTGATTGAAGCCAACTTCTACAGCTCTGCTGAGGCCCAGAAGCAAGGCTTCGATGTGCTGGACT
TGCACTTCCACTTCCGCCGCCACACGGAGAAGCACCTGCAGCCAGACGGCGTGCACTGGAATGAGTGCGCTCACCGGCAC
CTCTCCCAGCTGCTGCTGGCCCACGTGGCTGACGCCTGGGGGGTGGAGCTGCCCCAGCGCAACTCGGTGAGCAAGTGGAT
CAAGGGTGGCCCCGCGAGGGGAAGAGCTGGCGGGAGATGGGACAGACAGCCCCAGGCCTTCCCTCCGCCCCGCCCTTTGC
CTCTGCGGGGGCGTGGCCCCCTGCTCCCCTTGCCAGCTCCCCACTCAGTCCGTTTCCCAGTCCCGCCCCCACCACCTCAT
CCCTTCCCCAGTCGCCAGGTGATGCCCCCGTTTGTGCCCTATCGCCAAGATGCCTGTTTTTCTTCAGACCATCATTTCCA
GGAGGATCCGTTTTCCTTAAACCATTTCCATTCAGGTGCCTCCCCATCCACCCAGACAGAATTTGCCTTCGAGGCTGACT
TTGTGTTTGGTCCTCAGCCGCCCATGCCCCCCTTACCCCTACCCAGTCAGCAGTGCGCCCCCGTGGTCCATAGGGGTTTT
CCCCGGTATCATCCCCGTGGTCCGTACATGCCCAGGAGAGGGCCGCCCAGGCCTTCCAGAAGAAGGGCCCCAGCCCATCC
AGAGCCAAAGCCTCAATAG

Alignment

ORF - retro_sscr_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.16 %
• Parental protein coverage: 73.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          MVH.....VQQLLHNKFVVILGDS.QRAVYKDLVLLLQK..LLT..QLKAKGE.SFEQD.LV.GGQ.G..
Retrocopy MVHLWTADVQQLLHNKFVVILGDSVQRAVYKDLVLLLQKNDLLTLSQLKAKGEHSFEQDRLVSGGQQGRM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEGVLEELTCGP-APDLVIINSCLWDLSRYGRCSMEA
          HNG.QYREVRQFC..S.HHLVRFYFLTRVYS.YLE..LEEL..G..APDLVI.NSCLWDL.RYG..S...
Retrocopy HNGIQYREVRQFC--SDHHLVRFYFLTRVYSDYLEDILEELQSGEHAPDLVIMNSCLWDLTRYGEDSWPS

Parental  YRENLERVFVRMDQVLPDSCLLVWNMAMPLGERVTGGFLLPELQPLAG-SLRRDVVEGNFYSATLAGDHC
          Y..NLE..F.R...VLP.SCL.VWN.AMP.G...T.GF..PEL...A...L...V.E.NFYS...A....
Retrocopy YLRNLESLFGRLHHVLPESCLFVWNTAMPVGDNITSGFIPPELRATASLHLKIQVIEANFYSSAEAQKQG

Parental  FDVLDLHFHF-RHAVRHRHRDGIHWDQHAHRHLSHLLLTHVADAWGVELPKRDYPPDPWTEDWPEPDHLF
          FDVLDLHFHF.RH...H...DG.HW...AHRHLS.LLL.HVADAWGVELP.R......W....P......
Retrocopy FDVLDLHFHFRRHTEKHLQPDGVHWNECAHRHLSQLLLAHVADAWGVELPQRN-SVSKWIKGGPARGRAG

Parental  QGSQGQPPDFGEQLALPPPSSLP-PPMPFPSPLPQPSPLPLFPPLPQEPPFFPGQPF
          .....QP..F.....LP.....P..P.P.P.....P.P.P...P.P......P..P.
Retrocopy GRWDRQPQAFPPPRPLPLRGRGPLLPLPAPHSVRFPVPPPPPHPFPSRQVMPPFVPY

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	1.59 RPM	66.23 RPM
SRP014902_testis	7.78 RPM	111.60 RPM
SRP018288_heart	1.07 RPM	11.60 RPM
SRP018288_kidney	0.69 RPM	28.07 RPM
SRP018288_liver	0.16 RPM	8.00 RPM
SRP018288_lung	4.38 RPM	30.14 RPM
SRP018856_adipose	0.80 RPM	56.10 RPM
SRP035408_brain	0.16 RPM	42.05 RPM
SRP035408_liver	0.18 RPM	5.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_23 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_23 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23 ,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,