RetrogeneDB ID: retro_sscr_459

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:69163690..69164368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LCLAT1
• Ensembl ID: ENSSSCG00000025901
• Aliases: None
• Description: Sus scrofa lysocardiolipin acyltransferase 1 (LCLAT1), mRNA. [Source:RefSeq mRNA;Acc:NM_001142845]

Sequence

>retro_sscr_459
GACTATTTTTGCGATTTCCATGAACCACTTCAACTCCTCATATTCCTAGAAGGAACTGATTTCACAGAAAACAGCGTAGT
TCAAAATAATGAATTTGCTGAAAAGAATGGACTTCTGAAATATGCCTATGTCTTACATTCAAGAACCACAGGCTTTACTT
TGGTAGCAGACTGTGTAAGAGAAGGTAAAAATCTGCATGCTGGCCGTGACTTCATGGTGACAAACCCTCACAACACACCT
CAGACAGAGAGACACCTTCTCCTTGGGGGCTTTCCCAAAGAGATCCACTTCCATGTCCACTGACACCGGTGGACACCCTC
CCCTTGTCCAGAGAGGACCTCCAGCTCTGGTGCCACAAACAATGGTAAGAGAAAGAAAGAGGCTGTGCCCCTTCTATTGA
GGGGAGAAGAATTTTTACTTTAGGGGACAGACTATCATTCTACTTGTAAATCTAAGCCCAGAGTCCTTGTTTGAGGTCAA
ATTGCTTTCTACTGGACCCTGTTCAGCCCTGCAATGTGCCTGTTCATCTGTTTATACAGTATTGTTTGGTGGTATTTTAT
AATCATCACTGTCATTTTTGTGCTGCAGGAGAGAATATTTGGTGGACTAGAGATCATCAAACTTGCATGTAAACTTTTTT
TTTTTTAATACAAACAGTCACATTTAAATGCAAAGAAA

Alignment

ORF - retro_sscr_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DYFCNIHEPLQLLIFPEGTDLTENSTARSNEFAEKNGLQKYEYVLHPRTTGFTFVVDRLREGKNLDAVHD
          DYFC..HEPLQLLIF.EGTD.TENS....NEFAEKNGL.KY.YVLH.RTTGFT.V.D..REGKNL.A..D
Retrocopy DYFCDFHEPLQLLIFLEGTDFTENSVVQNNEFAEKNGLLKYAYVLHSRTTGFTLVADCVREGKNLHAGRD

Parental  ITVAYPHNIPQTERHLLLGDFPKEIHFHVHRY-PVASLPASKEDLQLWCHKRWEEKE-ARLRSFYRGEKN
          ..V..PHN.PQTERHLLLG.FPKEIHFHVH...PV..LP.S.EDLQLWCHK.W.EKE..RL..FY.GEKN
Retrocopy FMVTNPHNTPQTERHLLLGGFPKEIHFHVH*H<PVDTLPLSREDLQLWCHKQW*EKE<KRLCPFY*GEKN

Parental  FAFTGQTVI-PPCKSELRVLVVKWLSILYWTLFSPAMCLLIYFYSLARWYFIIIIVILVLQERLFGGLEL
          F.F.GQT.I...CKS..RVLV.......YWTLFSPAMCL.I..YS...WYFIII.VI.VLQER.FGGLE.
Retrocopy FYFRGQTII<STCKSKPRVLV*GQIA-FYWTLFSPAMCLFICLYSIVWWYFIIITVIFVLQERIFGGLEI

Parental  IELAC--YRFLHKQPHLNAKK
          I.LAC.......KQ.HLNAKK
Retrocopy IKLACKXXXXXYKQSHLNAKK

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	5.04 RPM
SRP014902_testis	0.00 RPM	4.24 RPM
SRP018288_heart	0.00 RPM	9.19 RPM
SRP018288_kidney	0.00 RPM	4.14 RPM
SRP018288_liver	0.00 RPM	6.72 RPM
SRP018288_lung	0.00 RPM	5.09 RPM
SRP018856_adipose	0.00 RPM	0.60 RPM
SRP035408_brain	0.00 RPM	0.38 RPM
SRP035408_liver	0.00 RPM	1.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_459 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000025901	1 retrocopy	retro_sscr_459 ,
Tursiops truncatus	ENSTTRG00000013682	1 retrocopy	retro_ttru_1032,