RetrogeneDB ID: retro_ocun_1437

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:22004959..22005804(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024518
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSOCUG00000000392
• Aliases: None
• Description: armadillo repeat containing 1 [Source:HGNC Symbol;Acc:17684]

Sequence

>retro_ocun_1437
ATGAATTCTTCCTCCTCTACTATGAATGAAGAACCTGATGCTCTATCAGTAGTTAACCAGCTACGAGATCTAGCAGCAGA
TCCATTAAATAGACGAGCCATCGTCCGGGACCAGGGATGTCTGCCTGGCCTTATTCTGTTTATGGACCATCCCAACCCCC
CTGTGGTCCACTGGGCTTTGCTCGCTCTTCAATACTTGGCGGAATGCCGTGCAAACAGAGAGAAGATGAAGGGGGAACTG
GGTATGATATTGAGTTTACAAAATGTTATACAGAAAACTACAACTCCAGGAGAAACAAAACTCCTGGCCTCTGCAATCTA
TGACATTTTTCAGTCCTCTAATATGGCAGATGGCGATAGCTTCAGTGAAATGAATTCACGTCGAAGGAAATCTCAGTTTT
TTCTGGGAACTACAAACAAGCGTGCAAAACAGTGGTTTTGCATATAGATGGTCTTGATGATACGTCTCAAAGAAATCTAT
GTGAAGAGGCTTTGTTAAAAATTAAAGGTGTTATTAGCTTTACTTTTCAAATGGCTGTTCAAAGATGTGTGGTGCGAATC
CGTTCAGATTTGAAGGCGGAGGCTGTGGCATCAGCGATAGCATCAACCAAGGTTATGAAAGCTCAGCAAGTTGTGAAAAG
TGGAAGTGGAGAAGAGATGCTGGTCCCGCTCCAGGATACTCCTGTGGAAGTAGAGCAGAACGCAGAGCTGCCTGACTACC
TGCCGGAGGATGAGAGTGCCACCAAGGAGCAGGACACAGCAGTGTCCCCGGTCCGCTCACACCCGGAGGGTGGAACTAGC
TGGCTGAGCACAGCGGCAAACTTTTTATCCAGGTCATTTTACTGG

Alignment

ORF - retro_ocun_1437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSSSTMNEEPDALSVVNQLRDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAECR
          MNSSSSTMNEEPDALSVVNQLRDLAADPLNRRAIV.DQGCLPGLILFMDHPNPPVVH.ALLAL.YLAECR
Retrocopy MNSSSSTMNEEPDALSVVNQLRDLAADPLNRRAIVRDQGCLPGLILFMDHPNPPVVHWALLALQYLAECR

Parental  ANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFSEMNSRRRKAQFFLGTTNK
          ANREKMKGELGM.LSLQNVIQKTTTPGETKLLAS.IYDI.QSSNMADGDSFSEMNSRRRK.QFFLGTTNK
Retrocopy ANREKMKGELGMILSLQNVIQKTTTPGETKLLASAIYDIFQSSNMADGDSFSEMNSRRRKSQFFLGTTNK

Parental  RA-KTVVLHIDGLDDTSRRNLCEEALLKIKGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQ
          RA.KTVVLHIDGLDDTS.RNLCEEALLKIKGVISFTFQMAVQRCVVRIRSDLKAEA.ASAIASTKVMKAQ
Retrocopy RA<KTVVLHIDGLDDTSQRNLCEEALLKIKGVISFTFQMAVQRCVVRIRSDLKAEAVASAIASTKVMKAQ

Parental  QVVKSESGEEMLVPFQDTPMEVEQNTELPDYLPEDESPTKEQDKAVSRVGSHPEGGASWLSTAANFLSRS
          QVVKS.SGEEMLVP.QDTP.EVEQN.ELPDYLPEDES.TKEQD.AVS.V.SHPEGG.SWLSTAANFLSRS
Retrocopy QVVKSGSGEEMLVPLQDTPVEVEQNAELPDYLPEDESATKEQDTAVSPVRSHPEGGTSWLSTAANFLSRS

Parental  FYW
          FYW
Retrocopy FYW

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
SRP017611_brain	0.28 RPM	17.16 RPM
SRP017611_kidney	0.10 RPM	9.02 RPM
SRP017611_liver	0.08 RPM	6.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1437 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1437 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437 , retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,