RetrogeneDB ID: retro_ocun_1838

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019231:83605..84534(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSOCUG00000017699
• Aliases: None
• Description: ariadne homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:690]

Sequence

>retro_ocun_1838
CTGGCTCAGGACTGTCCACTTCGTACACCAGAGGACTTTGTGTTTCCGTTGCTTCCCAATGAAGAACTGAGAGACAAATA
CAGGTCCTACCTCTTCCGGGACTATGTGGAGAGTCATTACCAGCTCCAGCTGTGTCCTGGTGCAGACTGTCCCATGGTTA
TTCGAGTACAGGAGCCTAGAGCTCGCCGAGTGCAGTGCAATCGGTGCAACGAAGTCTTCTGTTTCAAGTGTCGTCAGATG
TATCACGCCCCCACAGACTGCGCCACAATCCGGAAATGGCTCACGAAGTGTGCAGACGACTCTGAAATGGCCAACTACAT
TAGTGCCCACACTAAAGACTGTCCCAAGTGCAACATCCGCATTGAGAAGAATGGAGGCTGCAATCACATGCAATGCTCCA
AGTGTAAACACGACTTCTGCTGGATGTGTCTAGGAGACTGGAAGACTCATGGCAGTGAATACTATGAGTGCAGTCGGTAC
AAGGAGAATCCTGACATTGTCAACCAAAGCCAGCAAGCCCAGGCCAGGGAGGCCCTCAAGAAGTACTTGTTCTACTTTGA
GAGGTGGGAAAACCACAACAAAACTTGCAGCTAGAGGCGCAGACATACCAGCGGATTCATGAAAAGATTCAAGAGAGGGT
TATGAATAACCTGGGGACGTGGATCGACTGGCAGTATCTACAGAACGCTGCCAAGCTCTTGGCCAAGTGTCAGTACACTC
TGCAATACACCTATCCCTATGCGTACTACATGGAGTCTGGACCCAGGAAGAAGCTGTTTGAATACCAGCAGGCTCAGCTG
GAGGCTGAGATCAAAAATCTGTCATGGAAAGTGGAGCGTGCTGACAGCTATGACCGAGGGGACTTGGAGAACCAGATGCA
TATAGCAGAGCAGCGGAGGAGAACCCTGCTGAAGGATTTCCATGACACC

Alignment

ORF - retro_ocun_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.43 %
• Parental protein coverage: 62.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQDCPLRTPEDFVFPLLPNEELRDKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCN
          .AQDCPLRTPEDFVFPLLPNEELRDKYR.YLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCN
Retrocopy LAQDCPLRTPEDFVFPLLPNEELRDKYRSYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCN

Parental  EVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFC
          EVFCFKCRQMYHAPTDCATIRKWLTKCADDSE.ANYISAHTKDCPKCNI.IEKNGGCNHMQCSKCKHDFC
Retrocopy EVFCFKCRQMYHAPTDCATIRKWLTKCADDSEMANYISAHTKDCPKCNIRIEKNGGCNHMQCSKCKHDFC

Parental  WMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNK-SLQLEAQTYQRIHEK
          WMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNK..LQLEAQTYQRIHEK
Retrocopy WMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNK<NLQLEAQTYQRIHEK

Parental  IQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVE
          IQERVMNNLGTWIDWQYLQNAAKLLAKC.YTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEI.NLSWKVE
Retrocopy IQERVMNNLGTWIDWQYLQNAAKLLAKCQYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIKNLSWKVE

Parental  RADSYDRGDLENQMHIAEQRRRTLLKDFHDT
          RADSYDRGDLENQMHIAEQRRRTLLKDFHDT
Retrocopy RADSYDRGDLENQMHIAEQRRRTLLKDFHDT

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	0.66 RPM	26.32 RPM
SRP017611_kidney	0.20 RPM	28.79 RPM
SRP017611_liver	0.08 RPM	15.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1838 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1838 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013035	1 retrocopy	retro_amel_1021,
Callithrix jacchus	ENSCJAG00000003305	1 retrocopy	retro_cjac_1106,
Homo sapiens	ENSG00000177479	1 retrocopy	retro_hsap_1876,
Gorilla gorilla	ENSGGOG00000017134	1 retrocopy	retro_ggor_1373,
Myotis lucifugus	ENSMLUG00000013946	1 retrocopy	retro_mluc_1869,
Mustela putorius furo	ENSMPUG00000014344	1 retrocopy	retro_mputfur_610,
Mus musculus	ENSMUSG00000064145	1 retrocopy	retro_mmus_795,
Nomascus leucogenys	ENSNLEG00000006710	1 retrocopy	retro_nleu_1228,
Oryctolagus cuniculus	ENSOCUG00000017699	1 retrocopy	retro_ocun_1838 ,
Pongo abelii	ENSPPYG00000013890	1 retrocopy	retro_pabe_1557,
Pan troglodytes	ENSPTRG00000014902	1 retrocopy	retro_ptro_1259,
Ictidomys tridecemlineatus	ENSSTOG00000001766	1 retrocopy	retro_itri_1047,