RetrogeneDB ID: retro_sscr_654

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:159523239..159523974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMN1
• Ensembl ID: ENSSSCG00000016970
• Aliases: None
• Description: Sus scrofa survival of motor neuron 1, telomeric (SMN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001130735]

Sequence

>retro_sscr_654
CAGTACACTCTAAAGAATAGTGACATTTCTGAAGCTTCAGATAAACCAAAAGGCACACCTAAAAGATAACCTGCTAAGAA
GAATAAAAGCCAAAAAAATAATACCATAGCTCCCTTGAAGCAGTGGAAGGTTGGTGACAGATATTCTGCTGTTTGGTTGG
AAGATGGCTGCATTTACCCAGCTACCATTGCTTTGATTGATTTTAAGAGAGAAACCTGTATTGTGTTTTACAATGTATAT
GGAAATAGAGAAAAGCAAAATCTGTCTGATTTACTTTCCCGGCCTTGGATGTAGCTAACAATATAGAAGAGAATGCTCTG
GAGAATGAAAATGAAAGTCAAATTTCCACAGATGAAAGTGAGAGCTCATCCAGATCTCCTGGAAGTAAGTCAAGTAACAT
AAAGTCAAAAGCTGCTCCATGGAACTCTTTTCTCCTTCCACCACTCCCTATGCCAGGAGCAGGTCTTGGACCAAGAAAGC
CAGGTCTAAAATTCAATGGCCCACCACCACCACTGCTGCTGCCAACACCGCTACACTTCCTGTTATGCTGGCTGCCTCCA
TTTCCTTCTGGACCACCAATAATTCCCCCACACACCTCCTATATGACCAGATTCTCTGGATGATGCTGATGCTTTGAGAA
GTATGTTAATCTCTCAGTACATGAATGGCTATCATACTGGTTACTATATGGGTTTCAAACAAAATCAAAAAGAAGGAAGG
TGCTCACATTTCAAT

Alignment

ORF - retro_sscr_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 82.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHALKNGDISEASDKPKATPKRKPPKKNKSQKKNTTASLKQWKVGDRCSAIWSEDGCIYPATIASIDFKR
          ...LKN.DISEASDKPK.TPKR.P.KKNKSQK.NT.A.LKQWKVGDR.SA.W.EDGCIYPATIA.IDFKR
Retrocopy QYTLKNSDISEASDKPKGTPKR*PAKKNKSQKNNTIAPLKQWKVGDRYSAVWLEDGCIYPATIALIDFKR

Parental  ETCIVVYTGYGNREEQNLSDLLS-PTSEVANNIEENAQENENESQISTDESESSSRSPGNKPNNIKSKAA
          ETCIV.Y..YGNRE.QNLSDLLS.P...VANNIEENA.ENENESQISTDESESSSRSPG.K..NIKSKAA
Retrocopy ETCIVFYNVYGNREKQNLSDLLS<PALDVANNIEENALENENESQISTDESESSSRSPGSKSSNIKSKAA

Parental  PWNSFLPPPPPMPGAGLGPRKPGLKFNGPPPP--PPPPPHFLSCWLPPFPSGPPIIPP-PPPICPDSLDD
          PWNSFL.PP.PMPGAGLGPRKPGLKFNGPPPP...P.P.HFL.CWLPPFPSGPPIIPP..PPI.PDSLDD
Retrocopy PWNSFLLPPLPMPGAGLGPRKPGLKFNGPPPPLLLPTPLHFLLCWLPPFPSGPPIIPP>TPPI*PDSLDD

Parental  ADALGSMLISWYMSGYHTGYYMGFKQNQKEGRCSHFN
          ADAL.SMLIS.YM.GYHTGYYMGFKQNQKEGRCSHFN
Retrocopy ADALRSMLISQYMNGYHTGYYMGFKQNQKEGRCSHFN

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	9.69 RPM
SRP014902_testis	0.00 RPM	22.35 RPM
SRP018288_heart	0.00 RPM	17.08 RPM
SRP018288_kidney	0.00 RPM	37.83 RPM
SRP018288_liver	0.00 RPM	25.59 RPM
SRP018288_lung	0.00 RPM	27.29 RPM
SRP018856_adipose	0.09 RPM	33.25 RPM
SRP035408_brain	0.00 RPM	30.39 RPM
SRP035408_liver	0.00 RPM	20.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_654 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654 ,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,