RetrogeneDB ID: retro_sscr_680

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:115190467..115191004(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG4
• Ensembl ID: ENSSSCG00000015020
• Aliases: None
• Description: B-cell translocation gene 4 [Source:HGNC Symbol;Acc:13862]

Sequence

>retro_sscr_680
TACTCTAACGGCCTTTCTAATGGGTAAGGCTTCAGGTGTATTAGGATAAATAATTAGAATAACCACCCCCACCCCGAAAG
GACTTGTGCTGAAAATGAAGTGGATTTTTCTCACCTGTGTCTTCCAAACGAGATGACCATCTATGTAGATCACTTTGAAG
TGTTCTGTAGATACGGTGAGAAAAATCACCCATTTATAATGGCTAATTTAAAAGGCAGATTGGAGGAATGAAAACTCTCG
AAATAAAACAGTTATGATTTTGGGAAATCTGTGTTGAACTATTCCAGCATTTCCTCCAATGGAAAAAGTTGCTACAGAAA
ACCTCAGCTAATTCCTGAAGTCAGCATTCCAGAGAGTATTTATCAGGTTGAAAACTTGAAGCAGCCCTTTCAGTGTTGAT
TCCAAATTCCCTGAAAAACTAATATGATGATGACCAGGGCTCACTTGGAAATATTTTTCATGTGTTGGCATAAGAACCCT
CAAGGTCATAGGCTTTCTGCTATACAAAGAGTAGAGAGGTACCACTGGGTCACAACA

Alignment

ORF - retro_sscr_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 79.48 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HSDHPSKGQAFRCIRINNNQTKDPILERACAESNVDFSHLGLPKEMTIWVDPFEVCCRYGEKNRPFTIAS
          .S...S.G..FRCIRINN.....P..ER.CAE..VDFSHL.LP.EMTI.VD.FEV.CRYGEKN.PF..A.
Retrocopy YSNGLSNG*GFRCIRINN*NNH-PHPERTCAENEVDFSHLCLPNEMTIYVDHFEVFCRYGEKNHPFIMAN

Parental  FKGRWEEWELSQQISDAVNRATLDYSSGTSSDEESCNKEPQIIPKVINPKSIYQVENLKQPFQTWFQMPR
          .KGR.EE..LS...S.......L.YSS..SS...SC...PQ.IP.V..P.SIYQVENLKQPFQ..FQ.P.
Retrocopy LKGRLEE*KLSK*NSYDFGKSVLNYSS-ISSNGKSCYRKPQLIPEVSIPESIYQVENLKQPFQC*FQIP*

Parental  KRNMVDGRMGLLRNAYHVLHKTPKGHRPPAAHRVDRYHWVNT
          K.NM...R...L.......HK.P.GHR..A..RV.RYHWV.T
Retrocopy KTNMMMTR-AHLEIFFMCWHKNPQGHRLSAIQRVERYHWVTT

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.10 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	0.38 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_680 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_680 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1324
Equus caballus	retro_ecab_299

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014210	2 retrocopies	retro_cfam_1324, retro_cfam_471,
Choloepus hoffmanni	ENSCHOG00000000032	1 retrocopy	retro_chof_2674,
Equus caballus	ENSECAG00000012564	1 retrocopy	retro_ecab_299,
Monodelphis domestica	ENSMODG00000014496	1 retrocopy	retro_mdom_1647,
Sus scrofa	ENSSSCG00000015020	1 retrocopy	retro_sscr_680 ,
Tursiops truncatus	ENSTTRG00000010435	1 retrocopy	retro_ttru_1303,