RetrogeneDB ID: retro_sscr_322

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:87524971..87525606(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSSSCG00000022858
• Aliases: None
• Description: Citrate synthase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00889]

Sequence

>retro_sscr_322
ATGCCCTTGTACCTCACCATCCACAGTGACCATGAAGGTGGCAGTCTAAATGCTTATACCAGCCATTTGGTGGGCAGTGC
CTTTTCAGACCCCTACTTGTCCTTTGCAGCAGCCATGAATGGGCTGACAGGGCCCTTACATGGACTGGCAGGCAAATCAG
GAAGTGCTTGTTTGGCTGACACAGCTACAGAAAGAAGTTGGCAAAGATGTATCAGATGAGAAGTTATGAGACTACATCTG
GAACACACTCAACTCAGGACAGGTTGTCCCAGGCTATGGCCATGCAGTACTAAGGAAGACTGATCCACAAGATACCTGTC
AAAAGAGAGTTTGCTCTGAAACGCCTGCCTCATGACCCCGTGTTTAAGCTGGTTGCTCAGCTGTACGAGATTGTGCCCAA
TGTCCTCCTGGAGCAGGGCAAGGCCAAGAATCCTTGGCCCAATGTGGATGCTCACAGTGGGGTGCTGCTCCAGTACTATG
GCATGACGGAGATGAACTACTACACAGTCCTGTTCAGGGTATCACGGGCACTGGGTGTATTAGCATAGCTCATCTGGAGC
TGAGCCTTAGGCTTCCCTCTAGAGAGGCCCAAGTCCATGAGCACAGATGGTCTGATGAAATTTGTGGACTCTAAG

Alignment

ORF - retro_sscr_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLA-GP-LHGLANQEVLVWLTQLQKEVGKD
          M.LYLTIHSDHEGG...A.TSHLVGSA.SDPYLSFAAAMNGL..GP.....ANQEVLVWLTQLQKEVGKD
Retrocopy MPLYLTIHSDHEGGSLNAYTSHLVGSAFSDPYLSFAAAMNGLT>GPYMDWQANQEVLVWLTQLQKEVGKD

Parental  VSDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQ-REFALKHLPHDPMFKLVAQLYKIVPNVLLEQ
          VSDEKL.DYIWNTLNSG.VVPGYGHAVLRKTDP..TCQ.REFALK.LPHDP.FKLVAQLY.IVPNVLLEQ
Retrocopy VSDEKL*DYIWNTLNSGQVVPGYGHAVLRKTDPQDTCQ>REFALKRLPHDPVFKLVAQLYEIVPNVLLEQ

Parental  GKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLIKLV
          GKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLF.VSRALGVLA.LIWS.ALGFPLERPKSMSTDGL.K.V
Retrocopy GKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFRVSRALGVLA*LIWS*ALGFPLERPKSMSTDGLMKFV

Parental  DSK
          DSK
Retrocopy DSK

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	20.31 RPM
SRP014902_testis	0.00 RPM	20.93 RPM
SRP018288_heart	0.05 RPM	94.14 RPM
SRP018288_kidney	0.00 RPM	24.92 RPM
SRP018288_liver	0.16 RPM	17.27 RPM
SRP018288_lung	0.00 RPM	9.88 RPM
SRP018856_adipose	0.35 RPM	169.42 RPM
SRP035408_brain	0.00 RPM	18.01 RPM
SRP035408_liver	0.00 RPM	10.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_322 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_322 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322 ,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,