RetrogeneDB ID: retro_sscr_687

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:145804932..145805295(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSSSCG00000006559
• Aliases: None
• Description: Sus scrofa jumping translocation breakpoint (JTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001128468]

Sequence

>retro_sscr_687
CAAGCAGAAGCTTCCGTGCAAGAGGAGAAACTTTCAGTGAGCACCTCAAATTTGCCATCCTGGCTAGTGGAAGAGTTTGT
GGTGGCAGAAGAGTGTGCTCCATGCTCTAATTTCCAGTCTAAAACCACCCCTGAGTGTGGTTCCCCAGGGTATGTGGAGA
AAATCATGTGCAGCTCATCTAAGAGGATCGAGTTCAACAGCTGCTGCTCAGCTCTGATGGAACAACACTTATTCTGGAAA
TTTTGGAAATTCGAAGGGGCTGTTGTAGGTGTAGCCTTGGTCTTTGCTTGCCTTGTCATTGTGCGTCAGTGACAACTGGA
CAGAAAGGCTCTGGAAAAGGTCCGGCAGCAAACTGAGTCCATA

Alignment

ORF - retro_sscr_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAEAPVREEKLSVSTSNLRCWLVEEFVVAEECAPCSNFQAKTTPECSSTGYVEKITCSSSKRNEFKSCRS
          QAEA.V.EEKLSVSTSNL..WLVEEFVVAEECAPCSNFQ.KTTPEC.S.GYVEKI.CSSSKR.EF.SC.S
Retrocopy QAEASVQEEKLSVSTSNLPSWLVEEFVVAEECAPCSNFQSKTTPECGSPGYVEKIMCSSSKRIEFNSCCS

Parental  ALMEQHLFWKF---EGAVVGVALVFACLVIVRQRQLDRKALEKVRKQIESI
          ALMEQHLFWKF...EGAVVGVALVFACLVIVRQ.QLDRKALEKVR.Q.ESI
Retrocopy ALMEQHLFWKFWKFEGAVVGVALVFACLVIVRQ*QLDRKALEKVRQQTESI

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	10.62 RPM
SRP014902_testis	0.00 RPM	52.48 RPM
SRP018288_heart	0.03 RPM	22.40 RPM
SRP018288_kidney	0.00 RPM	26.70 RPM
SRP018288_liver	0.00 RPM	20.95 RPM
SRP018288_lung	0.00 RPM	16.70 RPM
SRP018856_adipose	0.12 RPM	32.94 RPM
SRP035408_brain	0.00 RPM	15.44 RPM
SRP035408_liver	0.00 RPM	17.03 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_687 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002520	1 retrocopy	retro_chof_1297,
Callithrix jacchus	ENSCJAG00000009973	1 retrocopy	retro_cjac_496,
Dasypus novemcinctus	ENSDNOG00000000740	1 retrocopy	retro_dnov_1095,
Echinops telfairi	ENSETEG00000008256	1 retrocopy	retro_etel_1340,
Felis catus	ENSFCAG00000012590	2 retrocopies	retro_fcat_1025, retro_fcat_1838,
Myotis lucifugus	ENSMLUG00000013299	1 retrocopy	retro_mluc_2225,
Oryctolagus cuniculus	ENSOCUG00000011788	1 retrocopy	retro_ocun_470,
Procavia capensis	ENSPCAG00000003210	1 retrocopy	retro_pcap_301,
Pongo abelii	ENSPPYG00000000791	1 retrocopy	retro_pabe_1886,
Sus scrofa	ENSSSCG00000006559	1 retrocopy	retro_sscr_687 ,
Tupaia belangeri	ENSTBEG00000012646	1 retrocopy	retro_tbel_762,