RetrogeneDB ID: retro_sscr_52

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:63332353..63333223(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012383
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSSSCG00000006120
• Aliases: None
• Description: OTU domain containing 6B [Source:HGNC Symbol;Acc:24281]

Sequence

>retro_sscr_52
ATGGAAGATTCCCAGAGTGAGCATCAACGGATGATACGACGCCACAACCGCGAGAAGAAAGAGCTGCAGGCCCGTATCCA
GAGCATGAAGAACTCGGTCCCCAGGAGTGACAAGAAGAGAAGAAAGCAGATGCTCCTAGATGTGGCCCGCCTTGAGGCTG
AGATGGAGCAGAAGCACCAGCAAGAGCTGGAGAAGTTCCAGGAGAGTTTCCCTGGTAACCTCGATTCTGTCACTGAAGAT
CTGGCCAAGATGGATCTCGAGAACCAGCCTCCCCGCCCCTCGAGGGCCCAGAGAAGGCGCGAAAGAAGAGCGGCCCTCGC
GAGGGAGCGTCAGGAGAGGATCGCCGAGGCCGAGATGGAGCATCTGGCCAGCTTCCGCAAGGATGAGGAAGAGAAGCTCC
GCGCCATCCTGGGGGCCAAGAATCTGGAGATGAAGGATATCCCGGCCGACGGCCACTGCATGTACCGCGCCATCCAAGAC
CAGCTGGTGTTCTCGGTGACCGTGGAGAGCCTGCGGAGACGCACCGCTGAGTACATGCAGAAGCACGTCGACGACTTCCT
GCCTTTCTTCAGCGACCCCGAAACCGGCGACTCCTACAGCCGCGACGACTTCTTGAGCTACTGCGACGACATCGTGCGCA
GCGCGTCGTGGGGAGGCCAGCTCGAGCTGAGGGCCCTGTCGCACATCCTGCAGACCCCTATCGAGGTGATCCAGGCCAAC
TCGCCCGCCGTCGTTATCGGAGAGGAGTACACCAAGAGGCCGCTCATCCTGGTCTATATGCGATACGCCTGCAGCCTCGG
GGAGCACTACAACTCCGTGAAGCCTCTTGAGGCCGGAGCCGTCGGGGGCGCTCCACCGCGTCTCTTCTAG

Alignment

ORF - retro_sscr_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.51 %
• Parental protein coverage: 55.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTEELDEEEQLVRRHRKEKKELQAKIQSMKNVVPKNDKKRRKQLTEDVAKLEAEMEQKHRKELEQLKLTS
          ......E.....RRH..EKKELQA.IQSMKN.VP..DKKRRKQ...DVA.LEAEMEQKH..ELE.....S
Retrocopy MEDSQSEHQRMIRRHNREKKELQARIQSMKNSVPRSDKKRRKQMLLDVARLEAEMEQKHQQELEKFQ-ES

Parental  KESKIDSVAVNISNLVLENQPLRISKAQKRREKKAALEKEREERIAEAEIENLTGARHVESEKLAQILGA
          .....DSV........LENQP.R.S.AQ.RRE..AAL..ER.ERIAEAE.E.L...R..E.EKL..ILGA
Retrocopy FPGNLDSVTEDLAKMDLENQPPRPSRAQRRRERRAALARERQERIAEAEMEHLASFRKDEEEKLRAILGA

Parental  RQLEIKQIPSDGHCMYRAIEDQL
          ..LE.K.IP.DGHCMYRAI.DQL
Retrocopy KNLEMKDIPADGHCMYRAIQDQL

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	2.26 RPM
SRP014902_testis	0.85 RPM	15.70 RPM
SRP018288_heart	0.00 RPM	38.03 RPM
SRP018288_kidney	0.00 RPM	32.41 RPM
SRP018288_liver	0.00 RPM	16.47 RPM
SRP018288_lung	0.10 RPM	23.93 RPM
SRP018856_adipose	0.00 RPM	14.70 RPM
SRP035408_brain	0.03 RPM	21.18 RPM
SRP035408_liver	0.00 RPM	15.73 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_52 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_52 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_52 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_350
Oryctolagus cuniculus	retro_ocun_29

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52 ,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,