RetrogeneDB ID: retro_sscr_433

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:52820283..52820727(-)
• Located in intron of: ENSSSCG00000010053

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM195A
• Ensembl ID: ENSSSCG00000007995
• Aliases: None
• Description: family with sequence similarity 195, member A [Source:HGNC Symbol;Acc:14142]

Sequence

>retro_sscr_433
ATGTACACCATCACCAAGGGACCAAGCAAGCTGGTCCCATAGCACCGCACAGGTCCCACACACCAGCAGGTGGAGAGCAG
GCTCCTCGAGCTCCTGAAATGCTACTAGCATCCTGAGCAACCAACCCTGCAACCCCCACGGACACAGCCTCCAGGACCCT
GGCCCTTGTCAAGTCCAGGGCTGAGGCTTGTGTTCAATCGGGTGAATGGCCGGTGGACTCCTGCCACATCCCCATCCCTC
GAGGGAATCCAAGAGACGTAAACATCGGCCCACGAGGAGAACATCCGATTTGTGTCTGAAGCCTGGCAGCAAGTGGAGCA
GCAGCTGGGTGGTGGCCCAGCCAGTGAGAGTGGGCCAAGGCCTGTGCAGTACGTGGAGAGGACCCCCAACCCCCGGCTAC
AGAACTTCATGCCCATCAACCTGGATGAGTGGTGGGCACAGGAG

Alignment

ORF - retro_sscr_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYTITKGPSKLVAQRRTGPTQQQVENRLGELLKCR-HPAPPTPQPPRTQPPGPWPLSSPGPRLVFNRVNG
          MYTITKGPSKLV...RTGPT.QQVE.RL.ELLKC..HP..PT.QPPRTQPPGPWPLSSPG.RLVFNRVNG
Retrocopy MYTITKGPSKLVP*HRTGPTHQQVESRLLELLKCY*HPEQPTLQPPRTQPPGPWPLSSPGLRLVFNRVNG

Parental  RRPPATSPSLEGSQETYTLAHEENVRFVSEAWQQVEQQLGGGPAGESGPRPVQYVERTPNPRLQNFVPID
          R..PATSPSLEG.QET.T.AHEEN.RFVSEAWQQVEQQLGGGPA.ESGPRPVQYVERTPNPRLQNF.PI.
Retrocopy RWTPATSPSLEGIQET*TSAHEENIRFVSEAWQQVEQQLGGGPASESGPRPVQYVERTPNPRLQNFMPIN

Parental  LDEWWAQQ
          LDEWWAQ.
Retrocopy LDEWWAQE

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	7.43 RPM
SRP014902_testis	0.00 RPM	11.88 RPM
SRP018288_heart	0.00 RPM	51.50 RPM
SRP018288_kidney	0.00 RPM	59.10 RPM
SRP018288_liver	0.00 RPM	59.65 RPM
SRP018288_lung	0.00 RPM	5.40 RPM
SRP018856_adipose	0.18 RPM	4.14 RPM
SRP035408_brain	0.00 RPM	6.96 RPM
SRP035408_liver	0.00 RPM	28.89 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_433 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011979	1 retrocopy	retro_cjac_932,
Homo sapiens	ENSG00000172366	1 retrocopy	retro_hsap_4901,
Gorilla gorilla	ENSGGOG00000013784	1 retrocopy	retro_ggor_43,
Nomascus leucogenys	ENSNLEG00000008117	1 retrocopy	retro_nleu_1269,
Pan troglodytes	ENSPTRG00000007548	1 retrocopy	retro_ptro_3268,
Sus scrofa	ENSSSCG00000007995	1 retrocopy	retro_sscr_433 ,