RetrogeneDB ID: retro_ocun_1322

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:112571756..112572293(+)
• Located in intron of: ENSOCUG00000015032

Retrocopy information

• Ensembl ID: ENSOCUG00000020911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HAUS2
• Ensembl ID: ENSOCUG00000011004
• Aliases: None
• Description: HAUS augmin-like complex, subunit 2 [Source:HGNC Symbol;Acc:25530]

Sequence

>retro_ocun_1322
ATGGCTGCTGCCAGCCCCTGGGGCCTGGCGCCAGAGCCAGGTGTTGCTGGGCCACTGTGGAGCCACTTCGTAGCTTCAGG
GATAGCCGCTGAGGAGATTTTAAGTGTGCCTAAGGGAACAGACCCTTGCTTTGTGGACTTCTCTGAACTACGACAGATCA
CAAACACTCAAGCTGAAATACACCAGAAAAACCTGGAAATCAAACTCCCGAAACTAGAAAAAGATAAAGCAGATGTTGTT
CACCCCTTGTTTTCGGCTCAGAAGTGTCATAGTCTGCAAAGCATGAATAGTCATTTAGAAGCAGTGCTAAAAGAAACGAG
GTCTCTCGGGCAGAGACTGTGGAAACCCATGTGCCGGGAAAACTTACCTATTGAAGTGGTTTATCACAGATTTATGGTGC
ATTTGCTGGAGTTGGCTGTGACTTTCACTGAGAAACTAGAAACCCATCTTGAAACAATTAGAAATATTCCTCGTTTAGAT
GCAAATCTAACAAAAAGGAGCAAGGCTTTAGCAAGGGTCGATATTTTGGTGACTGAG

Alignment

ORF - retro_ocun_1322 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.65 %
• Parental protein coverage: 77.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAANPWDPAPEPNAAGLLLGHFVASGMVTEEILSISKKTDPCFVNFSRLQQITNIQAEISQKNLEIELL
          MAAA.PW..APEP..AG.L..HFVASG...EEILS..K.TDPCFV.FS.L.QITN.QAEI.QKNLEI.L.
Retrocopy MAAASPWGLAPEPGVAGPLWSHFVASGIAAEEILSVPKGTDPCFVDFSELRQITNTQAEIHQKNLEIKLP

Parental  KLEKDTADIVHPLYLAQKCHTLQSMNNHLEAVLKEKRSLRQRLLKPMCQENLPLEAVYHRYMVHLLELAV
          KLEKD.AD.VHPL..AQKCH.LQSMN.HLEAVLKE.RSL.QRL.KPMC.ENLP.E.VYHR.MVHLLELAV
Retrocopy KLEKDKADVVHPLFSAQKCHSLQSMNSHLEAVLKETRSLGQRLWKPMCRENLPIEVVYHRFMVHLLELAV

Parental  TFIEKLETHLETIRNIPHLDANLKKMSKALAKMDILVTE
          TF.EKLETHLETIRNIP.LDANL.K.SKALA..DILVTE
Retrocopy TFTEKLETHLETIRNIPRLDANLTKRSKALARVDILVTE

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	5.52 RPM
SRP017611_kidney	0.00 RPM	6.79 RPM
SRP017611_liver	0.00 RPM	1.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1322 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1322 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003587	4 retrocopies	retro_meug_1171, retro_meug_1231, retro_meug_702, retro_meug_996,
Microcebus murinus	ENSMICG00000000819	1 retrocopy	retro_mmur_648,
Monodelphis domestica	ENSMODG00000017882	1 retrocopy	retro_mdom_1473,
Oryctolagus cuniculus	ENSOCUG00000011004	1 retrocopy	retro_ocun_1322 ,
Sorex araneus	ENSSARG00000001275	2 retrocopies	retro_sara_123, retro_sara_413,
Ictidomys tridecemlineatus	ENSSTOG00000006207	1 retrocopy	retro_itri_618,
Vicugna pacos	ENSVPAG00000006260	1 retrocopy	retro_vpac_599,