RetrogeneDB ID: retro_ocun_599

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:16641646..16642564(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARFGAP2
• Ensembl ID: ENSOCUG00000002073
• Aliases: None
• Description: ADP-ribosylation factor GTPase activating protein 2 [Source:HGNC Symbol;Acc:13504]

Sequence

>retro_ocun_599
AAAAGCTCCATCATTGGCAAGAAGCCGGTAGCAGCTAAGAAAGGCCTGGGCGCCCAGAAGGTGAGCGGCCGGAGCTTCAG
CGAGATGGAGCGGCAGGCCCAGGTGGCAGAGGAGCTCCGTGAGCAGCAGGCGGCGCATGCTAAGAAGCAGGCCGAGGAGT
CCATGGTCGCCTCCATGCGTCTGGCCTACCAGGAGCTCCAGCTTGATCGGAAGGAGGAGGAGAAGCAGCTCCAGAATCTG
GAGGGGAAGAAGGGAGAGCAGGCGGAGCGGCTGGGCATGGGCTTGGTGAGCCGGAGCTCCGTGTCCCGCTCGGTGCTGTC
CGAGATGCAGGTGATCGAGCAGGAGATCCCAGTGACCGCCAAGTCCTCCCGCTCGCAACTGGACCTGTTTGACGACGTTT
GGACGTTCACCTCTGGACCTCCAAAGTACAAGGACAACCCCTTTTCCTTGGGGGAAAGTTTTGGTTCCCGCTGGGATACG
GATACCACCTGGGGCATGGACAGGGTAGAGGAGAAGGAGGCAGAAGTGACCATCTCGAGCATCCGGCCCATTTCGGAAAG
AGCCACAAACCGGAGGGACGTGGAGAGCCGGAGTTCGGGCCTCGAGTCCAGCGAAGCAGGCCAGAAGTTTGCAGGTGCAA
AAGCCATCTCATCCGACATGTTCTTTGGGCGGGAGGTGGACGTTGAGTATGAAGCCAGGTCTCGGCTGCAGCAGCTCACG
GGCAGCAGTGCCATCAGCTCTTCAGACCTCTTTGGGGACGTGCATGGAGCCCATGCAGCAGGAAGCATGTCTCTGGGCAA
TGTGCTCCCCTCGGCGGACATCGCCCAGTTTAAGCAGGGTGTCAAGTCTGTGGCTGGCAAGATGGCTGTGCTGGCCAATG
GTGTGATGAATTCTTTGAAGGATCACTACGGTTCCTAC

Alignment

ORF - retro_ocun_599 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 58.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKPAAAKKGLGAKKGLGAQKVSSQSFSEIERQAQVAEKLREQQVADAKKQAEESMVASMRLAYQELQLDR
          K.....KK...AKKGLGAQKVS..SFSE.ERQAQVAE.LREQQ.A.AKKQAEESMVASMRLAYQELQLDR
Retrocopy KSSIIGKKPVAAKKGLGAQKVSGRSFSEMERQAQVAEELREQQAAHAKKQAEESMVASMRLAYQELQLDR

Parental  KKEEKQLQNLEGKKREQAERLGMGLVSRSSVSHSVLSEMQVIEQETPVTAKSSRSQLDLFDDVGTFASGP
          K.EEKQLQNLEGKK.EQAERLGMGLVSRSSVS.SVLSEMQVIEQE.PVTAKSSRSQLDLFDDV.TF.SGP
Retrocopy KEEEKQLQNLEGKKGEQAERLGMGLVSRSSVSRSVLSEMQVIEQEIPVTAKSSRSQLDLFDDVWTFTSGP

Parental  PKYKDNPFSLGESFGSRWDTDTTWGMDRVEEKEPEVTISSIRPISERATNRRDVESRSSGLESSEARQKF
          PKYKDNPFSLGESFGSRWDTDTTWGMDRVEEKE.EVTISSIRPISERATNRRDVESRSSGLESSEA.QKF
Retrocopy PKYKDNPFSLGESFGSRWDTDTTWGMDRVEEKEAEVTISSIRPISERATNRRDVESRSSGLESSEAGQKF

Parental  AGAKAISSDMFFGREVDVEYEARSRLQQLAGSSAISSSDLFGDMDGAHGAGSVSLGNVLPSADIAQFKQG
          AGAKAISSDMFFGREVDVEYEARSRLQQL.GSSAISSSDLFGD..GAH.AGS.SLGNVLPSADIAQFKQG
Retrocopy AGAKAISSDMFFGREVDVEYEARSRLQQLTGSSAISSSDLFGDVHGAHAAGSMSLGNVLPSADIAQFKQG

Parental  VKSVAGKMAVLANGVMNSLQDRYGSY
          VKSVAGKMAVLANGVMNSL.D.YGSY
Retrocopy VKSVAGKMAVLANGVMNSLKDHYGSY

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	0.39 RPM	70.53 RPM
SRP017611_kidney	0.41 RPM	100.65 RPM
SRP017611_liver	1.62 RPM	239.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_599 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_599 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019965	1 retrocopy	retro_cjac_415,
Macropus eugenii	ENSMEUG00000004984	1 retrocopy	retro_meug_1841,
Microcebus murinus	ENSMICG00000007019	1 retrocopy	retro_mmur_51,
Mus musculus	ENSMUSG00000027255	1 retrocopy	retro_mmus_2776,
Oryctolagus cuniculus	ENSOCUG00000002073	2 retrocopies	retro_ocun_1769, retro_ocun_599 ,