RetrogeneDB ID: retro_meug_987

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold25226:11010..12429(+)
• 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_987
ATGCACCCCAGCGCCCCCAGCTACCCCACGGCCTCGCTGTACGTGGGGGACCTGCACCCCGAGGTGAGCGAGGCGATGCT
GTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGCGTCTGCAGGGACATGATCACCCGGCGCTCCCTGGGCT
ACGCCTATGTCAACTTCCAGCAGCCGGCCGACGCCGAGCGAGCCCTGGAGACCATGAATTTCGATGTCATCAAGGGCAAG
CCGGTGCGCATCATGTGGTCCCAGAGGGACCCCTCCCTCCGCAAGAGCGGCGTGGGCAACATCTTCATCAAAAACCTGGA
TAAGTCCATTGATAATAAGGCTTTGTTTGATACTTTCTCTGCCTTCGGGAACATCCTCTCCTGTAAAGTGGTATGTGATG
AAAATGGGTCCAAGGGCTATGGATTTGTACACTTTGAGACACGAGAGGCTGCTGAGAGGGCCATCGACAAAATGAACGGG
ATGCTTCTGAATGACCGCAAGGTCTTCGTGGGGCGCTTTAAATCCCGCAAAGAGAGGGAGGCAGAGCTCGGGGCCAGGGC
CAAAGAGTTCACCAACGTTTACATCAAGAACTTTGGCGAGGACATGGACGATCTGAGACTCAAGAGGCTCTTTGGTAAGT
TTGGACCTGCTTTAAGTGTCAAAGTCATGACTGATGAAAGTGGCACGTCCAAAGGGTTTGGCTTTGTGAACTTTGAGAGG
CACGAAGATGCCCAAAAGGCTGTAGATGAGATGAATGGAAAAGAACTGAATGGGAAAAAAATCTATGTGGGCCGGGCTCA
GAAAAAAGTAGAGCGCCAGACAGAACTGAAACGCAAATTTGAACAGATGAAGCAGGACAGGATCACCAGGTACCAGGGTG
TGAACCTGTACGTGAAAAATCTGGATGATGGGATTGATGATGAGCGCCTGCGCAAGGAGTTCTCTCCATTTGGTACCATC
ACCAGTGCAAAGGTGATGATGGAAGGGGGCCGCAGCAAAGGGTTCGGCTTCGTGTGCTTCTCCTCGCCAGAGGAAGCCAC
CAAAGCCGTCACAGAAATGAATGGCAGGATCGTGGCCACCAAGCCGTTGTACATAGCTTTAGCCCAGCGAAAAGAGGAGC
GGCAGGCTCATCTCACAAACCAGTACATGCAGAGAATGGCCAGCGTCAGAGCTGTGCCCAACCCTGTGATCAACCCTTAC
CAGCCTCCTTCAGGTTACTTCATGGCAGCTATTCCTCAGACTCAGAACAGGCCTGCCTACTATCCTGCCAGCCAAATCGC
TCCTCTCAGACCGAGTCCTCGCTGGACTGCTCAGGGCGCCAGACCTCATCCATTCCAGAACCTGCCCGGTGCTATCCGCC
CAGCGGCTCCCAGGCCGCCATTCAGTACAATGAGACCAGCTTCTTCACAGGTGCCGCGA

Alignment

ORF - retro_meug_987 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.04 %
• Parental protein coverage: 76.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNASGPGYPMASLYVGDLHPDVTEAMLYEKFSAAGPIMSIRVCRDVSTRRSLGYAYINFQQPADAERALD
          M..S.P.YP.ASLYVGDLHP.V.EAMLYEKFS.AGPI.SIRVCRD..TRRSLGYAY.NFQQPADAERAL.
Retrocopy MHPSAPSYPTASLYVGDLHPEVSEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALE

Parental  TMNFEVIKGRPIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFGNILSCKVAYDENGSRGF
          TMNF.VIKG.P.RIMWSQRDP.LRKSG.GNIFIKNLD.SIDNKAL.DTFS.FGNILSCKV..DENGS.G.
Retrocopy TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALFDTFSAFGNILSCKVVCDENGSKGY

Parental  GFVHFETEDAANQAISTMNGMLLNDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQEI
          GFVHFET..AA..AI..MNGMLLNDRKVFVG.FKSR.EREAELGAR..EFTN.Y.KNF.E..DD..L...
Retrocopy GFVHFETREAAERAIDKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDLRLKRL

Parental  FSQFGKTLSVKVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFGGRVLYVGRAQKKTERQSELKRRF
          F..FG..LSVKVM.DE.G.S.GFGFVNFE.HE.AQKAV..MNGKE..G...YVGRAQKK.ERQ.ELKR.F
Retrocopy FGKFGPALSVKVMTDESGTSKGFGFVNFERHEDAQKAVDEMNGKELNGKKIYVGRAQKKVERQTELKRKF

Parental  EQMKQERVNRCQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATKAV
          EQMKQ.R..R.QGVNLYVKNLDD.IDDE.LRKEFSP.G.ITSAKVM.EGG.SKGFGFVCFSSPEEATKAV
Retrocopy EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVCTKPLYVALAQRKEERKAILTNQYMQRISVLRNINGPI---FPQPTNYFLPAIPQSPTRASF
          TEMNGRIV.TKPLY.ALAQRKEER.A.LTNQYMQR....R....P.......P..YF..AIPQ...R...
Retrocopy TEMNGRIVATKPLYIALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPPSGYFMAAIPQTQNRPAY

Parental  YSPSTVAPIQPAPRWTSFSPGSSDLFSLPAT--PQHSISNISTVRQASTQVPQ
          Y..S..AP..P.PRWT...........LP....P.......ST.R.AS.QVP.
Retrocopy YPASQIAPLRPSPRWTAQGARPHPFQNLPGAIRPAAPRPPFSTMRPASSQVPR

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_987 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_987 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,