RetrogeneDB ID: retro_meug_1165

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold3116:13876..15065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC1L
• Ensembl ID: ENSMEUG00000007905
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]

Sequence

>retro_meug_1165
ATGAACCCCAGCGCCCCCAGCTACCCTATGGCCTCGCCCTACGTGGGGAATCTGCACCCCGATGTGACCCAGGCGCTGCC
CTACGAGAAGTTCAGCCCCGCCGGGCCCATCCTCTCCGTCGGAGACATGCAGGGACATGATCACCCACCGCTCCCTGGAC
TACACCTATGTCAACTTCCAGCAGCCAGTGGACGCTGAACGGGCATTAGATACAATGAATTTTGATGTCATTAAGAGCAA
GCCAGCGCGTATCATGTGGTCTCAACGTGATCCATCACTACGTAAAAGTGGTGTGGGCAATATATTCATCAAAAATTTGG
ATGAATCCATTGATAATAAAGCATTGCATGATACATTTTCTGCTTTTGGAAACATCCTTTCTTGTAAGGTGGTGTGTGAT
GAAAATGGGTCACAGGGCTATGGATTTGTACATTTTGAGACAAAAGAAGCTGCTGAAAGAGCTATTGAAAAAATGAATGG
AATTCTTCTTAATGATCGAAAAGTCTTTGTTGGTCCATTTAAATCCCGTAAAGAGAGAGAAGCAGAACTTGGAGCTAGAA
AAAAAGAGTTCACCAATGTTTACGTCAAAAATTTTGGTGAAGACATGGATGATCAGAGACTTAAGGAGCTCTTTGGCAAG
TTTGGACCTGCTTTAAGTGTAAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGTTTTGGCTTTGTCAGCTTTGAAAG
ACATGAAGATGCACAAAAAGCTGTAGATGAGATGAATGGAAAAGAACTGAATGGAAAACAAATTTATGTTGGCCGAGCTC
AGAAAAAATTGGAAAGACAGATGGAACTCAAGTGCACATTTGAACAACTGAAGCAGGATAGGATCACCAGATACCAGGGT
GTTAACCTGTATGTGAAAAATCTTGATGATGGTATTGATGACGAACATCTGTGAAAGGAGTTCTCACCATTTGGTACAAT
CACTAGTGCAAACGTGATGATGGCAGGTGGCAGAAGCAAAGGGTTTGGGTTTCTATGCTTCTCTTCGCCAGAGGAAGCCA
CCAAAGCAATCATAGAAATGAATGGCAGGATTGTTGCCACTAAAGCATTGTATGTAGCTTTACCCCAGCGCAAAGAGGAG
CGGCAGGCTCACCTCACAAACCAGTATATGCAGAGAATGGCAAGTGTCAGACCTGTGCCCAACCCTGTG

Alignment

ORF - retro_meug_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNASGPGYPMASLYVGDLHPDVTEAMLYEKFSAAGPIMSI-RVCRDVSTRRSLGYAYINFQQPADAERAL
          MN.S.P.YPMAS.YVG.LHPDVT.A..YEKFS.AGPI.S....CRD..T.RSL.Y.Y.NFQQP.DAERAL
Retrocopy MNPSAPSYPMASPYVGNLHPDVTQALPYEKFSPAGPILSV>ETCRDMITHRSLDYTYVNFQQPVDAERAL

Parental  DTMNFEVIKGRPIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFGNILSCKVAYDENGSRG
          DTMNF.VIK..P.RIMWSQRDP.LRKSG.GNIFIKNLD.SIDNKAL.DTFS.FGNILSCKV..DENGS.G
Retrocopy DTMNFDVIKSKPARIMWSQRDPSLRKSGVGNIFIKNLDESIDNKALHDTFSAFGNILSCKVVCDENGSQG

Parental  FGFVHFETEDAANQAISTMNGMLLNDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQE
          .GFVHFET..AA..AI..MNG.LLNDRKVFVG.FKSR.EREAELGAR..EFTN.YVKNF.E..DD..L.E
Retrocopy YGFVHFETKEAAERAIEKMNGILLNDRKVFVGPFKSRKEREAELGARKKEFTNVYVKNFGEDMDDQRLKE

Parental  IFSQFGKTLSVKVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFGGRVLYVGRAQKKTERQSELKRR
          .F..FG..LSVKVM.DE.G.S.GFGFV.FE.HE.AQKAV..MNGKE..G...YVGRAQKK.ERQ.ELK..
Retrocopy LFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKLERQMELKCT

Parental  FEQMKQERVNRCQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATKA
          FEQ.KQ.R..R.QGVNLYVKNLDD.IDDE.L.KEFSP.G.ITSA.VM..GG.SKGFGF.CFSSPEEATKA
Retrocopy FEQLKQDRITRYQGVNLYVKNLDDGIDDEHL*KEFSPFGTITSANVMMAGGRSKGFGFLCFSSPEEATKA

Parental  VTEMNGRIVCTKPLYVALAQRKEERKAILTNQYMQRISVLRNINGPI
          ..EMNGRIV.TK.LYVAL.QRKEER.A.LTNQYMQR....R....P.
Retrocopy IIEMNGRIVATKALYVALPQRKEERQAHLTNQYMQRMASVRPVPNPV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1165 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1165 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007145	1 retrocopy	retro_meug_426,
Macropus eugenii	ENSMEUG00000007905	6 retrocopies	retro_meug_1165 , retro_meug_1229, retro_meug_1274, retro_meug_1343, retro_meug_419, retro_meug_987,
Microcebus murinus	ENSMICG00000000974	1 retrocopy	retro_mmur_42,
Myotis lucifugus	ENSMLUG00000006324	1 retrocopy	retro_mluc_509,