RetrogeneDB ID: retro_ocun_367

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:58044421..58045175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXA1L
• Ensembl ID: ENSOCUG00000000720
• Aliases: None
• Description: oxidase (cytochrome c) assembly 1-like [Source:HGNC Symbol;Acc:8526]

Sequence

>retro_ocun_367
CATGCCAGAGATCCAGAAGTTTTCTACACTAGTCCCAGAAGCCAGGTTGGCAGGTTGGCAGGAAGCTGTGCTGAGTTGTA
TAGGGCCTCCACAGAGAGGACACTTCACCAGAAAAAGCATGACATCAAACTCTTCAGTCCTTTTGTTATACCTCTGACCC
AGGCTCCGGGCTGCATTTCCTTCTTCATTGCCTTGACAGAGATGGCCAACTGTCCTGTGCCCAGCCTGTGGACAGGAAGC
TGCTGGTGGTTCCACGGTCCCCAGTATCTGATCCTATCTGCATTTTACTGATGGTGGTCACTGCTACAGTGTGGGGTCTC
CCGAAGCCAGGTGCTGAAACAGGTATGCAAAGTTCCTATTGTCAGTGGGTGGGAAACATTCTCAGAGCGATGCCTCTGGC
AGTTTTGCCCATAACCATCTTTTTTCCCCCTAGCAGTGTTTGTGTACTGGCTCTCCTCCAACCTGTTTTCCCTGGGCCAA
GTGGCCTGCCTCTGGGTTCCTGCTGCACACACTGTACTTAAAATGCCCCAGTGTGCTGCACATGACCCTGACAAATTGCC
TCCACTGGAAAGCTTCTTAAAGAGCTTCAAGAAAGGCTGGAAGAAAGCTAAGACTGCACATCAGTTATGCAAGCAGGAAT
GACACACGAGGAATCATTTGGAGCTAGCGGCCAGAGGTCCCTTAAGACAGACATTACTGAGAATCCTCTACTATGCCTGG
AAAGAACCATGCTTCCAACACCCCCAGCAGCAAA

Alignment

ORF - retro_ocun_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 59.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HNHVPEIQKFSARIREARLTGDHAELYRASSEMTLYQKKHDIKLLRPLILPLTQAPIFISFFIALREMAN
          H...PE....S.R..........AELYRAS.E.TL.QKKHDIKL..P...PLTQAP..ISFFIAL.EMAN
Retrocopy HARDPEVFYTSPRSXXXXXXXSCAELYRASTERTLHQKKHDIKLFSPFVIPLTQAPGCISFFIALTEMAN

Parental  LPVPSLQTGGLWWFQN-LTVSDPTYILPMVVTATMWGVLELGAETGMQSSDLQWMRNVLRVMPLAVLPIT
          .PVPSL.TG..WWF.....VSDP..IL.MVVTAT.WG....GAETGMQSS..QW..N.LR.MPLAVLPIT
Retrocopy CPVPSLWTGSCWWFHG<SPVSDPICILLMVVTATVWGLPKPGAETGMQSSYCQWVGNILRAMPLAVLPIT

Parental  IHFPS-AVFVYWLSSNLFSLGQVACLRIPAVRTVLKIPQRVVHDPDKLPPREGFIKSFKKGWKNAEMAHQ
          I.FP..AVFVYWLSSNLFSLGQVACL..PA..TVLK.PQ...HDPDKLPP.E.F.KSFKKGWK.A..AHQ
Retrocopy IFFPP>AVFVYWLSSNLFSLGQVACLWVPAAHTVLKMPQCAAHDPDKLPPLESFLKSFKKGWKKAKTAHQ

Parental  LRERERRMQNHLELAARGPLRQT-FTHNPLL-QPAKNHPSNTPKSK
          L...E....NHLELAARGPLRQT..T.NPLL..P.KNH.SNTP.SK
Retrocopy LCKQE*HTRNHLELAARGPLRQT<ITENPLL<MPGKNHASNTPSSK

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	34.88 RPM
SRP017611_kidney	0.00 RPM	59.09 RPM
SRP017611_liver	0.00 RPM	28.83 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_367 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_367 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_367 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012893	1 retrocopy	retro_mluc_2461,
Monodelphis domestica	ENSMODG00000005347	1 retrocopy	retro_mdom_1308,
Oryctolagus cuniculus	ENSOCUG00000000720	1 retrocopy	retro_ocun_367 ,
Otolemur garnettii	ENSOGAG00000000631	1 retrocopy	retro_ogar_2369,
Ictidomys tridecemlineatus	ENSSTOG00000003318	1 retrocopy	retro_itri_352,