RetrogeneDB ID: retro_sscr_690

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:157480939..157481332(-)
• Located in intron of: ENSSSCG00000014436

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOSPD1
• Ensembl ID: ENSSSCG00000012686
• Aliases: None
• Description: motile sperm domain containing 1 [Source:HGNC Symbol;Acc:25235]

Sequence

>retro_sscr_690
CTGACTCTGCACAGTCCTCATCAGTTTGCCTTAAAGGTCAAAGTGTTGGGAGCTACCCCAAATAAGCGTGTCGCCGTTGA
CGCTGCAGGGGCAGTAACGCCTCAGTGTTGCGTGGATGTTGCGACTTGTCACAGAGACGTTCGCTCCTGTCCCCGGCGTG
TAATGGACAAGTTCCGTCTCCAAGTTTCTGGGCAGAGCCAGGGGAAGGCGTCAGGAAGGAAAGAGGTGGTGGCTACTCTT
CTCTCGTGGGCACAAGAACAACAAAAGGAAGAGGAGGCAAAAGGCATAAAGGAACATTTATCTGCAAGTTTATTTTGTGA
GCAGTCGTTTCAACCAGAAGGCAGAACTGCCTCCTCGGGACCTCGGCCACTGACCGTCTTCCTGGGAGGGGTG

Alignment

ORF - retro_sscr_690 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 61.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVKPQCCVDIVIRHRDVRSCHYGVIDKFRLQVSEQSQRKA
          LTL..P..FALK.KVL..TPNK.V.VDAAGAV.PQCCVD....HRDVRSC...V.DKFRLQVS.QSQ.KA
Retrocopy LTLHSPHQFALKVKVLGATPNKRVAVDAAGAVTPQCCVDVATCHRDVRSCPRRVMDKFRLQVSGQSQGKA

Parental  LGRKEVVATLLPSAKEQQKEEEEKRIKEHLTESLFFEQSFQPENRTVSSGPSLLTVFLGVV
          .GRKEVVATLL..A.EQQKEEE.K.IKEHL..SLF.EQSFQPE.RT.SSGP..LTVFLG.V
Retrocopy SGRKEVVATLLSWAQEQQKEEEAKGIKEHLSASLFCEQSFQPEGRTASSGPRPLTVFLGGV

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	0.27 RPM	29.47 RPM
SRP014902_testis	0.14 RPM	15.98 RPM
SRP018288_heart	0.08 RPM	10.22 RPM
SRP018288_kidney	0.00 RPM	33.00 RPM
SRP018288_liver	0.16 RPM	57.57 RPM
SRP018288_lung	0.00 RPM	12.02 RPM
SRP018856_adipose	0.00 RPM	19.06 RPM
SRP035408_brain	0.13 RPM	10.35 RPM
SRP035408_liver	0.00 RPM	80.02 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_690 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_690 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690 ,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,