RetrogeneDB ID: retro_sscr_245

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:23228592..23229307(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000010891
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP1AR
• Ensembl ID: ENSSSCG00000009128
• Aliases: None
• Description: adaptor-related protein complex 1 associated regulatory protein [Source:HGNC Symbol;Acc:28808]

Sequence

>retro_sscr_245
AGGCCTCTTACTGAAGAAGAAACTGTTGCCCTAAAAGAGAAGCATTATGATTCTATTGTTGAAAAACAGAAAGATCTTGA
TATGAAATTCCAAAAGGAGTTAGCCTTCCAGGAAGAGAAGACTAGAAGAAGTTTTATACGCTGCACAGCGTGAAGCAGCC
AGGGCAGCAAAGCAGCGAAAGCTCTTGGAGCAAGAAAGACAGAGAGTTGTGCAGCGATGCCATCCTTCAAACAATGGAGA
GCATCAAAGTTCAGGACCAGAAGATGACTTTGAATCTTCTTTGAGAAATATAAAGTCACAATATGAAGTTTTCCGAAGTA
GTAGACTCTCATCAGATGCCACAGTTTTGACACCAAATATAGAAAGCAGTTGTGATTTAATGACCAAAACTAAATCAACT
AGTGGAAATGATGACAGTACATCTTTACATCTAGAATGGGAAGATGAAGAAGGAATGAATAGAATGCTACCCACGAGAGA
ACGGTCCAAAACAGAGGAAGGCATTCTCCGGGCAGCACTTAAGTACAGCAGCAAGAAGACTGGAAGTAATCCTACGTCAG
CCTCTGATGATTCCAGTGGGCTGGAGTGGGGAAATGATTTTGTTAGTGCCGAAATGGATGATAATGGCAATTCCGAGTAT
TCGGGATTTGTAAATCCTGTGTTAGAACTGTCTGATTCTGGCCTAAAGCAATATGACACAGATCAACAACAACGA

Alignment

ORF - retro_sscr_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPLTEEEIVDLREKHYDSIVEKQKDLDMKIQKELALQ-EEKLRLEEEALYAAQREAARAAKQRKLLEQER
          RPLTEEE.V.L.EKHYDSIVE..K..D........L....K.RLEE..LYAAQREAARAAKQRKLLEQER
Retrocopy RPLTEEETVALKEKHYDSIVE--KQKDLDMKFQKELA>SRKRRLEE-VLYAAQREAARAAKQRKLLEQER

Parental  QRVVQRYHPSNNGEYQSSGPEDDFESCLRNIKSQYEVFRSSRLSSDATVLTPNTESSCDLMTKTKSTSGN
          QRVVQR.HPSNNGE.QSSGPEDDFES.LRNIKSQYEVFRSSRLSSDATVLTPN.ESSCDLMTKTKSTSGN
Retrocopy QRVVQRCHPSNNGEHQSSGPEDDFESSLRNIKSQYEVFRSSRLSSDATVLTPNIESSCDLMTKTKSTSGN

Parental  DDSTSLDLEWEDEEGMNRMLPMRERSKTEEDILRAALKYSSKKTGSNPTSASDDSNGLEWENDFVSAEMD
          DDSTSL.LEWEDEEGMNRMLP.RERSKTEE.ILRAALKYSSKKTGSNPTSASDDS.GLEW.NDFVSAEMD
Retrocopy DDSTSLHLEWEDEEGMNRMLPTRERSKTEEGILRAALKYSSKKTGSNPTSASDDSSGLEWGNDFVSAEMD

Parental  DNGNSEYSGFVNPVLELSDSGLKQYDTDQQKR
          DNGNSEYSGFVNPVLELSDSGLKQYDTDQQ.R
Retrocopy DNGNSEYSGFVNPVLELSDSGLKQYDTDQQQR

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	11.28 RPM
SRP014902_testis	0.00 RPM	10.89 RPM
SRP018288_heart	0.00 RPM	9.56 RPM
SRP018288_kidney	0.10 RPM	20.10 RPM
SRP018288_liver	0.32 RPM	11.83 RPM
SRP018288_lung	0.00 RPM	17.21 RPM
SRP018856_adipose	0.00 RPM	7.34 RPM
SRP035408_brain	0.00 RPM	17.91 RPM
SRP035408_liver	0.00 RPM	16.23 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_245 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_245 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007262	2 retrocopies	retro_chof_1995, retro_chof_8,
Monodelphis domestica	ENSMODG00000005746	1 retrocopy	retro_mdom_160,
Oryctolagus cuniculus	ENSOCUG00000004413	1 retrocopy	retro_ocun_91,
Otolemur garnettii	ENSOGAG00000001631	1 retrocopy	retro_ogar_1054,
Sus scrofa	ENSSSCG00000009128	1 retrocopy	retro_sscr_245 ,