RetrogeneDB ID: retro_sscr_8

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:34429984..34430407(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000007119
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NXT2
• Ensembl ID: ENSSSCG00000012581
• Aliases: None
• Description: nuclear transport factor 2-like export factor 2 [Source:HGNC Symbol;Acc:18151]

Sequence

>retro_sscr_8
ATGGCATCCGTGGACTTCAAGACCTACGTGGACCAGGCCTGCCGCGCAGCCGAGGAGTTTGTGAACGTGTACTACAGCAC
CATGGACAAGCGGCGGAGGTTGCTGTCCCGCCTGTACACAGGCACTGCCACCCTGGTGTGGAACGGCAATGCCGTTTCGG
GACAAGAATCCTTGAGTGAGTTTTTTGAGATGTTGCCTTCCAGCGAGTTCCAGATCAACGTGGTAGACTGCCAGCCTGTC
CACGACGACGCCACACCGAGCCAGACCACTGTCCTCGTGGTCATCTGTGGGACGGTGAAGTTTGAGGGCAACAAGCAGCG
GGACTTCAACCAGAACTTCATCCTGACGGCCCAGGCCTCACCCAGCAACGCAGTATGGAAGATCGCCAGTGATTGCTTCC
GCTTCCAGGACTGGGCCTGCTAG

Alignment

ORF - retro_sscr_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVDFKTYVDQACRAAEEFVNIYYETMDKRRRALTRLYLDKATLIWNGNVVTGLEALTNFFEMLPSSEFQV
          SVDFKTYVDQACRAAEEFVN.YY.TMDKRRR.L.RLY...ATL.WNGN.V.G.E.L..FFEMLPSSEFQ.
Retrocopy SVDFKTYVDQACRAAEEFVNVYYSTMDKRRRLLSRLYTGTATLVWNGNAVSGQESLSEFFEMLPSSEFQI

Parental  NMLDCQPVHEQATQAQTTVLVVTSGTVKFDGNKQHYFNQNFLLTAQSTPNNTVWKIASDCFRFQDWA
          N..DCQPVH..AT..QTTVLVV..GTVKF.GNKQ..FNQNF.LTAQ..P.N.VWKIASDCFRFQDWA
Retrocopy NVVDCQPVHDDATPSQTTVLVVICGTVKFEGNKQRDFNQNFILTAQASPSNAVWKIASDCFRFQDWA

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	16.86 RPM	3.58 RPM
SRP014902_testis	33.10 RPM	19.80 RPM
SRP018288_heart	3.77 RPM	9.25 RPM
SRP018288_kidney	10.24 RPM	14.18 RPM
SRP018288_liver	6.72 RPM	30.38 RPM
SRP018288_lung	7.94 RPM	30.04 RPM
SRP018856_adipose	6.46 RPM	8.70 RPM
SRP035408_brain	6.96 RPM	3.30 RPM
SRP035408_liver	3.85 RPM	20.58 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_sscr_8 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW480152	34429969	34430168	100	199	0	199

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_8 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_80
Gorilla gorilla	retro_ggor_67
Pongo abelii	retro_pabe_101
Macaca mulatta	retro_mmul_140
Callithrix jacchus	retro_cjac_98
Mus musculus	retro_mmus_12
Rattus norvegicus	retro_rnor_254
Oryctolagus cuniculus	retro_ocun_210
Bos taurus	retro_btau_118
Canis familiaris	retro_cfam_1137

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017999	1 retrocopy	retro_amel_59,
Bos taurus	ENSBTAG00000020739	1 retrocopy	retro_btau_118,
Canis familiaris	ENSCAFG00000028574	1 retrocopy	retro_cfam_1137,
Callithrix jacchus	ENSCJAG00000007369	1 retrocopy	retro_cjac_98,
Cavia porcellus	ENSCPOG00000003310	1 retrocopy	retro_cpor_29,
Dipodomys ordii	ENSDORG00000010714	1 retrocopy	retro_dord_2,
Echinops telfairi	ENSETEG00000008002	2 retrocopies	retro_etel_1926, retro_etel_1979,
Felis catus	ENSFCAG00000002240	1 retrocopy	retro_fcat_20,
Homo sapiens	ENSG00000101888	1 retrocopy	retro_hsap_80,
Gorilla gorilla	ENSGGOG00000013593	1 retrocopy	retro_ggor_67,
Loxodonta africana	ENSLAFG00000007116	1 retrocopy	retro_lafr_124,
Microcebus murinus	ENSMICG00000014511	3 retrocopies	retro_mmur_149, retro_mmur_1531, retro_mmur_25,
Myotis lucifugus	ENSMLUG00000000631	3 retrocopies	retro_mluc_1513, retro_mluc_160, retro_mluc_473,
Macaca mulatta	ENSMMUG00000013204	1 retrocopy	retro_mmul_140,
Monodelphis domestica	ENSMODG00000021343	1 retrocopy	retro_mdom_1611,
Mustela putorius furo	ENSMPUG00000003973	1 retrocopy	retro_mputfur_74,
Mus musculus	ENSMUSG00000042271	1 retrocopy	retro_mmus_12,
Oryctolagus cuniculus	ENSOCUG00000008261	1 retrocopy	retro_ocun_210,
Procavia capensis	ENSPCAG00000008006	1 retrocopy	retro_pcap_9,
Pongo abelii	ENSPPYG00000020625	1 retrocopy	retro_pabe_101,
Pteropus vampyrus	ENSPVAG00000006149	1 retrocopy	retro_pvam_14,
Rattus norvegicus	ENSRNOG00000019168	2 retrocopies	retro_rnor_2365, retro_rnor_254,
Sorex araneus	ENSSARG00000009307	1 retrocopy	retro_sara_4,
Sus scrofa	ENSSSCG00000012581	1 retrocopy	retro_sscr_8 ,
Ictidomys tridecemlineatus	ENSSTOG00000005243	3 retrocopies	retro_itri_1138, retro_itri_141, retro_itri_793,
Tarsius syrichta	ENSTSYG00000001924	1 retrocopy	retro_tsyr_42,
Tursiops truncatus	ENSTTRG00000005115	1 retrocopy	retro_ttru_19,
Vicugna pacos	ENSVPAG00000007314	1 retrocopy	retro_vpac_624,