RetrogeneDB ID: retro_sscr_729

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:42560088..42560636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000022859
• Aliases: None
• Description: None

Sequence

>retro_sscr_729
ATGCCGGTGCTGAAGAAGACCCGTGCTGGTCAGCGGACCAGGTTCAAGGCATTTGTTGCCACCAGAGATTACAACCATAA
ACGTCGGTTTGGGCATCAGGTGCTCTAAGGAGGTAGCCACCGCCATTCGTGGGGCCATCATTCTGGCCAAACTCTCCACT
GTCCCCCTGCGGTGAGGCTACTGGGGGAACAAGGTCGCCAAGCCCCATACCGTCCCTTACAAGGTGACTGGCCGCTGTGG
CTCCGTGCTGGTGCGCCTCATCCCTGTCCCCAGGGGCACTGGTTGTCTCAGCCCCTGTGCTCAAGAAGCTACTGATGACG
GCGGGAATTGATGACTGCTACACCTCTGCCAGGGGCTGCACTGCCACCATGGGCAACTTCGCCAAGGCCACCTTTGATGT
CATTTCCAAGACATACAGCTGTCTCACTCCTGATCTCTCGAAAGGGACAGTGCTCACCAAGTCTCCGTATCAGGAATTCA
CTGACCATCTTGTGAAGACTCACACCAGAGTTTCCGTGCAGAGGACCCAGGCTCCAGCTGTGGCCACC

Alignment

ORF - retro_sscr_729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.32 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVQKQTRAGQRTRFKAFVAIGDYNG-HVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPH
          MPV.K.TRAGQRTRFKAFVA..DYN...VGLG..CSKEVATAIRGAIILAKLS.VP.R.GYWGNK..KPH
Retrocopy MPVLKKTRAGQRTRFKAFVATRDYNH>NVGLGIRCSKEVATAIRGAIILAKLSTVPLR*GYWGNKVAKPH

Parental  TVPCKVTGRCGSVLVRLIP-APRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKT
          TVP.KVTGRCGSVLVRLIP..P.G...VSAPV.KKLLM.AGIDDCYTSARGCTAT.GNFAKATFD.ISKT
Retrocopy TVPYKVTGRCGSVLVRLIP>SP-GALVVSAPVLKKLLMTAGIDDCYTSARGCTATMGNFAKATFDVISKT

Parental  YSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVAT
          YS.LTPDL.K.TV.TKSPYQEFTDHLVKTHTRVSVQRTQAPAVAT
Retrocopy YSCLTPDLSKGTVLTKSPYQEFTDHLVKTHTRVSVQRTQAPAVAT

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	1.06 RPM	0.27 RPM
SRP014902_testis	0.99 RPM	0.00 RPM
SRP018288_heart	17.84 RPM	0.50 RPM
SRP018288_kidney	13.20 RPM	0.49 RPM
SRP018288_liver	5.12 RPM	0.32 RPM
SRP018288_lung	11.81 RPM	0.31 RPM
SRP018856_adipose	0.68 RPM	0.48 RPM
SRP035408_brain	9.15 RPM	0.06 RPM
SRP035408_liver	12.71 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_729 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Choloepus hoffmanni	ENSCHOG00000012360	9 retrocopies	retro_chof_1056, retro_chof_2398, retro_chof_2545, retro_chof_2607, retro_chof_368, retro_chof_378, retro_chof_535, retro_chof_919, retro_chof_989,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Sus scrofa	ENSSSCG00000022859	8 retrocopies	retro_sscr_280, retro_sscr_293, retro_sscr_412, retro_sscr_486, retro_sscr_729 , retro_sscr_803, retro_sscr_950, retro_sscr_951,