RetrogeneDB ID: retro_sscr_134

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:202465138..202466087(+)
• Located in intron of: ENSSSCG00000027537

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSSSCG00000011000
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_sscr_134
GGTTCTGGCTCCCCCATGGATATCTTTGATATGTTTTTTGGAGGAGAAGGAAGGATGCAGAGAACGGAGAGGTAAAAATG
TTGTGCATCAACTCTCAGTGACTTTAGAAGATCTATGTAATGGTGCAACAAGGAAACTAGCTCTGCAGAAGAATGTGATT
TGTGGCAAATGTGAAGGCCAAGGTGGTAAGAAAGGAGCAGTAGAATGCTGTCCCAGTTGCCGAGGTACTGGAATGCAAAT
AAGAATTCATCAAATAGGATCTGGAATGGTTCAGCAAATTCAGCCTGTGTGCATGGAGTGCCAGGGCCATGGGGAGCAGA
TCAGTCCTAAAGACAGATGTAAAAGCTGCAATGGGAGGAAGATAGTTTGAGAAAAGAAAATCCTAGAAGTTCATATTGAC
AAAGATATGAAAGATGGCCAGAAGATAACATTCCACGGTGAGGGAGACCAAGAACCAGGACTGGAGCCAGGAAACATTAT
CATTGTTTTAGATCAGAAGGACCATGCCGTTTTTAGTCAACGAGGAGAAGACCTTTTTATGTGTATGGACATACAGCTGG
TTGAGGCATTGTGTGACTTCCAAAAGCCAGTGTCTATTCTTGACAACGGAACCACAGTCATCACTTCTCATTCAGGTCAG
ACTGTCAAGCATGGTGATATCGAGTGTGTGCTAAATGAAGGCATGCCAATTTATCGTAGACCATATGAAAAGGGCCACCT
AATTACTGAATTTAAGGTGAACTTTCCTGAGAATGGTTTTCTCTCCCCTAATAAACTCTCTTTGCTGGAAAAGCTCCTAC
CTGAGAGGAAGGAAGCAGAAGAGACTGATGAAATGGACCAGGTAGAACTAGTGGACTTAGATCCAAATCAGGAGAGATGA
CGCCTTTGCAATGGAGCATATGAAGATGATGAACATCATCCTCGGGGTGGGGTTCAGTGTCAGACCTCT

Alignment

ORF - retro_sscr_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 80.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFGSPMDIFDMFFGGGGRMQ-RERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVE
          G.GSPMDIFDM.F.GG.....RERRGKNVVHQLSVTLEDL.NGATRKLALQKNVIC.KCEG.GGKKGAVE
Retrocopy GSGSPMDIFDM-FFGGEGRM>RERRGKNVVHQLSVTLEDLCNGATRKLALQKNVICGKCEGQGGKKGAVE

Parental  CCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKD
          CCP.CRGTGMQIRIHQIG.GMVQQIQ.VCMECQGHGE.ISPKDRCKSCNGRKIV.EKKILEVHIDK.MKD
Retrocopy CCPSCRGTGMQIRIHQIGSGMVQQIQPVCMECQGHGEQISPKDRCKSCNGRKIV*EKKILEVHIDKDMKD

Parental  GQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVIT
          GQKITFHGEGDQEPGLEPG.IIIVLDQKDHAVF..RGEDLFMCMDIQLVEALC.FQKP.S.LDN.T.VIT
Retrocopy GQKITFHGEGDQEPGLEPGNIIIVLDQKDHAVFSQRGEDLFMCMDIQLVEALCDFQKPVSILDNGTTVIT

Parental  SHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEETDEM
          SH.GQ.VKHGDI.CVLNEGMPIYRRPYEKG.LI.EFKVNFPENGFLSP.KLSLLEKLLPERKE.EETDEM
Retrocopy SHSGQTVKHGDIECVLNEGMPIYRRPYEKGHLITEFKVNFPENGFLSPNKLSLLEKLLPERKEAEETDEM

Parental  DQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
          DQVELVD.DPNQER.R..NG.AYEDDEHHPRGGVQCQTS
Retrocopy DQVELVDLDPNQER*RLCNG-AYEDDEHHPRGGVQCQTS

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	39.02 RPM
SRP014902_testis	0.14 RPM	277.66 RPM
SRP018288_heart	0.13 RPM	136.97 RPM
SRP018288_kidney	0.20 RPM	262.62 RPM
SRP018288_liver	0.48 RPM	300.31 RPM
SRP018288_lung	0.31 RPM	178.91 RPM
SRP018856_adipose	0.00 RPM	183.71 RPM
SRP035408_brain	0.03 RPM	524.43 RPM
SRP035408_liver	0.03 RPM	143.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_134 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_134 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134 , retro_sscr_984,