RetrogeneDB ID: retro_ocun_1174

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:119350046..119350662(+)
• Located in intron of: ENSOCUG00000011775

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSOCUG00000003903
• Aliases: None
• Description: MLF1 interacting protein [Source:HGNC Symbol;Acc:21348]

Sequence

>retro_ocun_1174
CTGAAAACTCAGAAAAAAGAGATGTTTCATGGCAAAAGGAAGAAATCAAAAAGTGAAGCCACAGACTGAGGTATTTCTGA
CAGTGTGCACATTTGTTATCTAGAAGAAAAGAAAACCAGCAACAATGTGGAGTTACATATTGTTTTGTCTACATTTGAGA
AAACCTTTGAGAGTAAAAGAATTGAAAGAAAAATTGTAAAGAAGCCAGCAATATATCTAAATATTAAATAATTCATCAGG
TAGCTTACAGAAGTTCAGATGTTGAAGAATCTGACAAGGAGGAATACCTTAATGATTTCAGATATGGACAGTCAAAGGCA
TTGTTTGATTAAAGTCCCGGATGAACTGCTTCAGTTAGAAACACTACTGAAACAACTCAAACAAAAAAATGATGAACTTA
AGGAGAAAGTCTTCTCTTATCAATATTCTGTATTTTCTTATCTAATTTAAAACAACTTCATGAAGAGTGCTCAGATGTTA
TGAAGAAGAAAACCAATATGAAGGGCATGTATCATTCACTTGGCCTTCCAGCTCTGTTACTTAAAGCAAGAATGCTTTTG
GGAGCAGAAAACATTTGCAAAACATCAGCTGTCAATTAGAGATGCTCCTTGACCAG

Alignment

ORF - retro_ocun_1174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.46 %
• Parental protein coverage: 51.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METQKKETMSRGKRKKTSNEAGGSGISDSVHIWCLEGKKKSDLMELDIVLSACEKAIQEHKERIESKICK
          ..TQKKE.M..GKRKK...EA...GISDSVHI..LE.KK.S...EL.IVLS..EK.......RIE.KI.K
Retrocopy LKTQKKE-MFHGKRKKSKSEATD*GISDSVHICYLEEKKTSNNVELHIVLSTFEKTFES--KRIERKIVK

Parental  EAINKFHCNIKELIKMLKEAQMLKNLKRKNAKVIADIKKKRQRLVEVQDELLRLEPQLIQLQTKYDELKE
          ........NIK..I..L.E.QMLKNL.R.N...I.D....R..L..V.DELL.LE..L.QL..K.DELKE
Retrocopy KPA--IYLNIK*FIR*LTEVQMLKNLTRRNTLMISDMDSQRHCLIKVPDELLQLETLLKQLKQKNDELKE

Parental  RKSS-LRTAADFLSNLKQLYHEYSDLQEKEPDTKETYDSSSLPALLFKARTFLGAEN-HLQNINHQLENL
          ...S.L.....FLSNLKQL..E.SD...K....K..Y.S..LPALL.KAR..LGAEN.HLQNI..QLE.L
Retrocopy KVFS<LSIFCIFLSNLKQLHEECSDVMKKKTNMKGMYHSLGLPALLLKARMLLGAEN<HLQNISCQLEML

Parental  LDQ
          LDQ
Retrocopy LDQ

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	0.06 RPM	31.62 RPM
SRP017611_kidney	0.00 RPM	5.17 RPM
SRP017611_liver	0.00 RPM	6.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1174 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1174 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151725	1 retrocopy	retro_hsap_1096,
Gorilla gorilla	ENSGGOG00000011892	1 retrocopy	retro_ggor_862,
Microcebus murinus	ENSMICG00000013084	1 retrocopy	retro_mmur_836,
Macaca mulatta	ENSMMUG00000012176	1 retrocopy	retro_mmul_850,
Nomascus leucogenys	ENSNLEG00000010967	1 retrocopy	retro_nleu_1628,
Oryctolagus cuniculus	ENSOCUG00000003903	1 retrocopy	retro_ocun_1174 ,
Pongo abelii	ENSPPYG00000015238	1 retrocopy	retro_pabe_979,
Pan troglodytes	ENSPTRG00000016643	1 retrocopy	retro_ptro_697,