RetrogeneDB ID: retro_sscr_870

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:55842091..55842427(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM32A
• Ensembl ID: ENSSSCG00000013855
• Aliases: None
• Description: family with sequence similarity 32, member A [Source:HGNC Symbol;Acc:24563]

Sequence

>retro_sscr_870
ATGGAGGCCCACGAGCACGTCCAACAGGGGCCCCCGAAGCTGAAAGGCGGCCCTGAGCTCAGGGCGATCAGACGAAAGAA
GAAAAAGAAGGCCAAAGACAAGGCCAAACTCCCGGAAGGGATGGGAACCATTCGAAGGGACAAGGAGGAGAAGCCACCAG
GCCTGGACGTGGGGACCCCGGCCCAGGTGGCCTTCGAGAAGATGCAGGAGGAGCGGCAGGGGGAAAGGATCCCGAAGAAA
GCATCCCGAACCCACAGGCAGAGAGTTGAGGACTTCAACAGACACCTGGATACACTCACAGAGTACTTCGACCTTCCCAA
AGTCAGCTGGACCAAG

Alignment

ORF - retro_sscr_870 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDYEQVQRGPLKLKGVAELGVTKRKKKKKDKDKAKLLEAMGTSKKNEEEKRRGLDKRTPAQAAFEKMQE
          ME..E.VQ.GP.KLKG..EL....RKKKKK.KDKAKL.E.MGT.....EEK..GLD..TPAQ.AFEKMQE
Retrocopy MEAHEHVQQGPPKLKGGPELRAIRRKKKKKAKDKAKLPEGMGTIRRDKEEKPPGLDVGTPAQVAFEKMQE

Parental  KRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK
          .RQ.ERI.KKAS.TH.QRVEDFNRHLDTLTE..D.PKVSWTK
Retrocopy ERQGERIPKKASRTHRQRVEDFNRHLDTLTEYFDLPKVSWTK

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	24.29 RPM
SRP014902_testis	0.00 RPM	24.89 RPM
SRP018288_heart	0.00 RPM	34.94 RPM
SRP018288_kidney	0.00 RPM	70.63 RPM
SRP018288_liver	0.00 RPM	44.61 RPM
SRP018288_lung	0.00 RPM	59.98 RPM
SRP018856_adipose	0.00 RPM	90.31 RPM
SRP035408_brain	0.00 RPM	132.50 RPM
SRP035408_liver	0.00 RPM	76.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_870 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_870 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Homo sapiens	ENSG00000105058	4 retrocopies	retro_hsap_1116, retro_hsap_1950, retro_hsap_2541, retro_hsap_693,
Gorilla gorilla	ENSGGOG00000022418	4 retrocopies	retro_ggor_1420, retro_ggor_1587, retro_ggor_592, retro_ggor_872,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654,
Microcebus murinus	ENSMICG00000013721	3 retrocopies	retro_mmur_1449, retro_mmur_252, retro_mmur_500,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mustela putorius furo	ENSMPUG00000016048	1 retrocopy	retro_mputfur_1493,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017,
Nomascus leucogenys	ENSNLEG00000005441	3 retrocopies	retro_nleu_192, retro_nleu_2227, retro_nleu_2790,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Pan troglodytes	ENSPTRG00000010641	4 retrocopies	retro_ptro_1304, retro_ptro_1480, retro_ptro_497, retro_ptro_684,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,
Sus scrofa	ENSSSCG00000013855	2 retrocopies	retro_sscr_292, retro_sscr_870 ,
Tarsius syrichta	ENSTSYG00000009106	1 retrocopy	retro_tsyr_418,