RetrogeneDB ID: retro_ocun_1499

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:25959194..25960172(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022146
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAAF2
• Ensembl ID: ENSOCUG00000015466
• Aliases: None
• Description: dynein, axonemal, assembly factor 2 [Source:HGNC Symbol;Acc:20188]

Sequence

>retro_ocun_1499
GGTGGTCCCTGCCCCGAGAGGAGGGGACCTGTGTGTCCCCCCTTGCAGTGTAACCAGGATGAGGAAACCCTGACCCTGCT
CATTGGCGTGCCGCGCATCCAGCCGCAAAGCCTTCGAGGGGACGTGAGCCCCCTCGGGTACCACGTGTGCTTCTCCGCGC
AGGACTCGGCTTACTCCTTCCTTCTGCAGTTTGCGCCCGAGAATAAGCTGAGCACCAGAGAGCCGGTGATTAGCATTTCC
TCAGACAATGCCGTGATAGAACTGACCAAATCTCCGGGGAGCTATGGACACTGGAAGCAGTGGTTTTACGGCTTAAACGA
CGCATCTTTGGAGGAAAGGTTGTTTGTCAACGAAGAAAATGTTGATGAGTTTCTTGAAGAGGTTCTGAGCTGTCCAGTGA
GACAGACAGTGCCACCAAACCCACCGTTAATTGAAGTCCTTCAAGTTAATGATAAAAAGATTCAAATTCATGCAGAGGTA
CAAGAATCTAGTAACTCTGATAAGCTTCAAGGAAAGGAAGACAAAGTCAATGAAGGAAGTCATCTAACTGAAAAGGAAAA
TGTAGACCATCTTATCACTCGTACAACTGATTCTGACTCATCAATAGCAGCTAAAGCACTAGAAATAGACAGTTGTGGTT
CAACTGCAACTGAACAGGAGTCTCTCAATGCTTCTCAGATGCTATTTGAAAAATCTCAGAAACCTGAGTCAAAAATGGAA
CCTCAAGTTTTCAAAGAAATGAGTGCTACTTACTCAGCTGAAGAAAAAGACACTTCAAAAGAATCAGTACTAAATGAAGA
GAAAGAATTCCGTGGAGATCATCTATCTTCATTACTGACCACAACAGCAGTTCACAATATACCAGATTTTGACAGCCTAA
AAGAAACCAATATGCAGGATGGTAGTGTGCAGATTATTAAAGATCATGTGACTCACTGTGCATTCAGTTTTCAGAATTCC
TTGCTATATGACTTGGAC

Alignment

ORF - retro_ocun_1499 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGPCPERRGPVCPPLQCNQDEETLTLLIGVPRIQPQSLRGDVSPLGYHVCFSAQDSAYAFLLQFAPENKL
          GGPCPERRGPVCPPLQCNQDEETLTLLIGVPRIQPQSLRGDVSPLGYHVCFSAQDSAY.FLLQFAPENKL
Retrocopy GGPCPERRGPVCPPLQCNQDEETLTLLIGVPRIQPQSLRGDVSPLGYHVCFSAQDSAYSFLLQFAPENKL

Parental  STREPVISISSDNAVIELAKSPGSYGHWKQWFYGLNDASLEERLFVNEENVDEFLEEVLSCPVRQTVPPN
          STREPVISISSDNAVIEL.KSPGSYGHWKQWFYGLNDASLEERLFVNEENVDEFLEEVLSCPVRQTVPPN
Retrocopy STREPVISISSDNAVIELTKSPGSYGHWKQWFYGLNDASLEERLFVNEENVDEFLEEVLSCPVRQTVPPN

Parental  PPLIEVLQVNDKKIQIHAEVQESSNSDKLQGKEDRVNEGSHLTEKENVDHLITRTTDSDSSIAAKALEID
          PPLIEVLQVNDKKIQIHAEVQESSNSDKLQGKED.VNEGSHLTEKENVDHLITRTTDSDSSIAAKALEID
Retrocopy PPLIEVLQVNDKKIQIHAEVQESSNSDKLQGKEDKVNEGSHLTEKENVDHLITRTTDSDSSIAAKALEID

Parental  SCGSTATEQESLNASQMLFEKSQKPESKMEPQVFKEMSAAYSAEEKDTSKESVINEEKEFREDHLSSLLT
          SCGSTATEQESLNASQMLFEKSQKPESKMEPQVFKEMSA.YSAEEKDTSKESV.NEEKEFR.DHLSSLLT
Retrocopy SCGSTATEQESLNASQMLFEKSQKPESKMEPQVFKEMSATYSAEEKDTSKESVLNEEKEFRGDHLSSLLT

Parental  TKAVHNIPDFDSIKETNMQDGSVQIIKDHVTHCAFSFQNSLLYDLD
          T.AVHNIPDFDS.KETNMQDGSVQIIKDHVTHCAFSFQNSLLYDLD
Retrocopy TTAVHNIPDFDSLKETNMQDGSVQIIKDHVTHCAFSFQNSLLYDLD

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	0.00 RPM	5.79 RPM
SRP017611_kidney	1.22 RPM	6.28 RPM
SRP017611_liver	0.00 RPM	4.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1499 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1499 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000015466	1 retrocopy	retro_ocun_1499 ,