RetrogeneDB ID: retro_meug_419

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold11170:5966..7166(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMEUG00000009419
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_419
CCAGTGCATATCATGTGTTGTCAACGTGATCCATCACTACGTAAAAGTGGTGTGGGCAATAGATTCATCAAAAATTTGGA
TAAATCCATTGATAATAAAGTATTGTATGATACATTTTCTGCTTTTGGAAACATCCTTTCTGGTTAGGTGGTGTGTGATG
AAAATGGGTCAAAGGGCTATGGATTTGTACACTTTGAGACACAAGAAGCTGCTGAAAGAGCTATTGAAAAAATGAATGGA
ATGCTTCTTAATGATCGAAAAGTCTTTGTGGGTCGATTTAAATCCCGTAAAGAGAGAGAAGCAGAACTTGGAGCTAGAGC
AAAAGAGTTCACTAATGTTTACATCAAAAATTTTGGTGAAGACATGGATGATGAAAGACTTAAGGACCTCTTTGGCAAGT
TTGGACCTGCCTTAAGTGTAAAAGTAATGACTGATGGAAGTGGAAAATCCAAAGGTTTTGGCTTTGTGAGCTTTGAAAGA
CATGAAGATGCAGAAAAAGCTGTAGATGAGATGAATGGAAAAGAACTGAATGGAAAACAGATTTATGTTCGCCGAGCTCA
GAAAAAAGTGGAAAGACAAGCGGAACTCAAGCGCAAATTTGAACAAATGAAGCAGGATAGGATCACCAGATACCAGGGTG
TTAACCTGTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTGCGAAAGGAGTTCTCACCATTTGGTACAATC
ACTAGTGCAAAGGTGATGATGGAAGGTGGCCGCAGCAAAAGGTTTGGGTTTGTATGTTTCTCTTTGCCAGAGGAAGCCAC
CAAAGCAGTCACAGAAATGAATGGCAGGATTGTTGCCACTAAGCCATTGTATGTAGCTTTAGCCCAGCACAAAGAGGATC
AGCAGGCACACCTCACAAACCAGTATATGCAGAGAATGGCAAGTGTCAGAGCTGTGCCCAACCCTGTGATCAACCCCTAT
CAGCCTCCTTCAGGTTACTTCATGGCAGCTATTCCTCAGACTCAGAACCGTGCAGCATATCATCCTGCTAGCCAAATTGC
CCAACTCAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAGAACATGCCCGGTGCTATCCGCC
CAGCAGCTCCTAGGCCACCATTTAATACAATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACACAGCGTGTT

Alignment

ORF - retro_meug_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFGNILSCKVAYDENGSRGFGFVHFETEDA
          P..IM..QRDP.LRKSG.GN.FIKNLD.SIDNK.LYDTFS.FGNILS..V..DENGS.G.GFVHFET..A
Retrocopy PVHIMCCQRDPSLRKSGVGNRFIKNLDKSIDNKVLYDTFSAFGNILSG*VVCDENGSKGYGFVHFETQEA

Parental  ANQAISTMNGMLLNDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQEIFSQFGKTLSV
          A..AI..MNGMLLNDRKVFVG.FKSR.EREAELGAR..EFTN.Y.KNF.E..DD..L...F..FG..LSV
Retrocopy AERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSV

Parental  KVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFGGRVLYVGRAQKKTERQSELKRRFEQMKQERVNR
          KVM.D..G.S.GFGFV.FE.HE.A.KAV..MNGKE..G...YV.RAQKK.ERQ.ELKR.FEQMKQ.R..R
Retrocopy KVMTDGSGKSKGFGFVSFERHEDAEKAVDEMNGKELNGKQIYVRRAQKKVERQAELKRKFEQMKQDRITR

Parental  CQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATKAVTEMNGRIVCT
          .QGVNLYVKNLDD.IDDE.LRKEFSP.G.ITSAKVM.EGG.SK.FGFVCFS.PEEATKAVTEMNGRIV.T
Retrocopy YQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKRFGFVCFSLPEEATKAVTEMNGRIVAT

Parental  KPLYVALAQRKEERKAILTNQYMQRISVLRNINGPI---FPQPTNYFLPAIPQSPTRASFYSPSTVAPIQ
          KPLYVALAQ.KE...A.LTNQYMQR....R....P.......P..YF..AIPQ...RA.....S..A...
Retrocopy KPLYVALAQHKEDQQAHLTNQYMQRMASVRAVPNPVINPYQPPSGYFMAAIPQTQNRAAYHPASQIAQLR

Parental  PAPRWTSFSPGSSDLFSLPAT--PQHSISNISTVRQASTQVPQAGPHTQRV
          P.PRWT............P....P........T.R.AS.QVP.....TQRV
Retrocopy PSPRWTAQGARPHPFQNMPGAIRPAAPRPPFNTMRPASSQVPRV-MSTQRV

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_419 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_419 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,