RetrogeneDB ID: retro_ocun_274

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:16877828..16879277(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022333
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GALNT13
• Ensembl ID: ENSOCUG00000017645
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) [Source:HGNC Symbol;Acc:23242]

Sequence

>retro_ocun_274
GAAAAGATGAAGGAGATGTTTAAAATCAATCAGTTCAATTTAATGGCAAGTGAGATGATTGCACTCAACAGATCTTTACC
AGATGTTAGGCTAGAAGGGTGTAAAACAAAGGTGTATCCAGATAATCTTCCTACAACAAGTGTGGTGATTGTTTTCCACA
ATGAGGCTTGGAGCACACTTCTACGAACTGTTCATAGTGTCATTAATCGCTCACCAAGACACATGATAGAAGAAATTGTT
CTAGTAGATGATGCCAGTTAAAGAGATTTTGTGAAAAGACCCCTAGAGAGTTATGTGAAAAAATTAAAAGTCCCAGTTCA
TGTAATTCGAATGGAACAACGTTCTGGACTGATCAGAGCTAGGTTAAAAGGAGCTGCTGTGTCAAAAGGCCAAGTGATCA
CCTTTTTGGATGCTCATTGTGAGTGCACAGTGGGGTGGCTGGAGCCTCTCTTAGCCAGGATCAAACATGACAGGAGAACA
GTAGTCTGCCCTATCATTGATGTTATCAGCGATGATACTTTTGAATACATGGCAGGCTCTGATATGACCTATGGTGGGTT
CAACTGGAAGCTCAATTTCCGCTGGTATCCTGTTCCCCAAAGAGAAATGGATAGAAGGAAAGGTGATCGAACTCTTCCTG
TCAGAACACCTACAATGGCAGGAGGCCTTTTTTCAATAGACAGAGATTACTTTCAGGAAATTGGCACATATGATGCTGGA
ATGGATATTTGGGGAGGAGAAAGCCTAGAAATTTCCTTTAGGATTTGGCAGTGTGGAGGAACTTTGGAAATTGTTACATG
CTCACATGTTGGACATGTGTTTCAGAAAGCTACACCTTACACGTTTCCAGGAGGCACGGGGCAGATTATCAATAAAAATA
ACAGACGACTTGCAGAAGTGTGGATGGATGAATTCAAGAATTTTTTCTATATAATCTCTCCAGGTGTTACAAAGGTAGAT
TATGGAGATATATCATCGAGACTTGGTCTGAGACACAAGCTACAGTGCAAACCTTTCTCTTGGTACCTAGAGAATATTTA
TCCTGATTCTCAAATTCCATGTCACTATTTCTCATTGGGAGAGATTCGAAATGTAGAAACAAATCAGTGTCTTGATAACA
TGGCCAGAAAAGAGAATGAAAAAGTTGGAATTTTTAATTGTCATGGTATGGGAGGTAATCAGGTTTTCTTGTATACTGCC
AACAAAGAAATTAGAACAGATGACCTTTGCTTGGATGTTTCCAAACTTCATGGCCCAGTCACGATGCTCAAATGCCACCA
CCTAAAAGGCACCCAGCTCTGGGAGTATGACCCAGTGAAGTTAACCTTACGGCATGTGAACAGTAATCAGTGCCTGGACA
AAGCCACCGAAGAGGATAGCCAGGTGCCCAGCATTAGAGACTGCAGTGGAAGCCGGTCACAGCAGTGGCTTCTTCGAAAC
GTCACACTT

Alignment

ORF - retro_ocun_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.92 %
• Parental protein coverage: 86.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKMKELFKINQFNLMASDLIALNRSLPDVRLEGCKTKVYPDELPNTSVVIVFHNEAWSTLLRTVYSVINR
          EKMKE.FKINQFNLMAS..IALNRSLPDVRLEGCKTKVYPD.LP.TSVVIVFHNEAWSTLLRTV.SVINR
Retrocopy EKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVINR

Parental  SPHYLLSEVILVDDASERDFLKLTLENYVKNLEVPVKIIRMEERSGLIRARLRGAAASKGQVITFLDAHC
          SP.....E..LVDDAS.RDF.K..LE.YVK.L.VPV..IRME.RSGLIRARL.GAA.SKGQVITFLDAHC
Retrocopy SPRHMIEEIVLVDDAS*RDFVKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDAHC

Parental  ECTLGWLEPLLARIKEDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDR
          ECT.GWLEPLLARIK.DR.TVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDR
Retrocopy ECTVGWLEPLLARIKHDRRTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDR

Parental  TLPVRTPTMAGGLFSIDRNYFEEIGTYDAGMDIWGGENLEMSFRIWQCGGSLEIVTCSHVGHVFRKATPY
          TLPVRTPTMAGGLFSIDR.YF.EIGTYDAGMDIWGGE.LE.SFRIWQCGG.LEIVTCSHVGHVF.KATPY
Retrocopy TLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGESLEISFRIWQCGGTLEIVTCSHVGHVFQKATPY

Parental  TFPGGTGHVINKNNRRLAEVWMDEFKDFFYIISPGVVKVDYGDVSVRKTLRENLKCKPFSWYLENIYPDS
          TFPGGTG..INKNNRRLAEVWMDEFK.FFYIISPGV.KVDYGD.S.R..LR..L.CKPFSWYLENIYPDS
Retrocopy TFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRHKLQCKPFSWYLENIYPDS

Parental  QIPRRYYSLGEIRNVETNQCLDNMGRKENEKVGIFNCHGMGGNQVFSYTADKEIRTDDLCLDVSRLNGPV
          QIP..Y.SLGEIRNVETNQCLDNM.RKENEKVGIFNCHGMGGNQVF.YTA.KEIRTDDLCLDVS.L.GPV
Retrocopy QIPCHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFLYTANKEIRTDDLCLDVSKLHGPV

Parental  IMLKCHHMRGNQLWEYDAEKLTLRHVNSNQCLDEPSEEDKMVPTMQDCSGSRSQQWLLRNMTL
          .MLKCHH..G.QLWEYD..KLTLRHVNSNQCLD...EED..VP...DCSGSRSQQWLLRN.TL
Retrocopy TMLKCHHLKGTQLWEYDPVKLTLRHVNSNQCLDKATEEDSQVPSIRDCSGSRSQQWLLRNVTL

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	3.20 RPM	66.28 RPM
SRP017611_kidney	6.59 RPM	3.45 RPM
SRP017611_liver	2.39 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_274 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_274 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013917	1 retrocopy	retro_mmur_228,
Oryctolagus cuniculus	ENSOCUG00000016221	1 retrocopy	retro_ocun_1260,
Oryctolagus cuniculus	ENSOCUG00000017645	1 retrocopy	retro_ocun_274 ,
Otolemur garnettii	ENSOGAG00000016208	2 retrocopies	retro_ogar_2525, retro_ogar_3272,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671,
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854,