RetrogeneDB ID: retro_meug_1343

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold374992:539..1789(+)
• 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_1343
ATGAACGCAAGTGGCCCCGGCTACCCCATGGCGTCCCTCTAAGTGGGCAACCTGCACTCCAACGTGAACGAGTCCATGCT
GTACGAGAAGTTCTCAGCCGCAGGGCCCATCATGTCCATCCGCGTGTGCAGTGACGTGGCCATGCGCCGCTCCCTGGGTT
ATGCCTACATCAACTTCCAGCAGCCCTTTGAATGAGCCTTGGACACCATGAACTTTGAGGTAATCAAGGGTAGGCCCATC
TGTATCATGTGGTCCCAGCAGGATCCAGGACTCCGGAAATCAGGAATTGGCAACATCTTTATCAAGAATTTGGATGATTC
CATTGACAACAAAGCCCTGTATGACACCTTCTCTACCTTTTGGAACATCCTCTCTTGTAAGGTGGTATGTGATGAGAATG
GCTTCCAAGAATTTGGCTTTGTCTACTTTGGGACTGAGGATACTGCAAACCAAGCAATCAGCACTATGAATGGGATGCTA
CTTAATGACCAAAAAGTTTTTATGGGTCACTTCAAGTCTCTGCAGGAATGGGAGGCAAAACTGGGGGCACGAGTGTTGGA
GTTCACCAACATCTATGTCAAGAACTTCAAGGAAAATGTGGATGATCGGTGCCTTCAGGAACTCTTCTCCCAGTTTGGAA
AGACTCTAAGTGTGAAGGTGATGGTCGATGAAAATGGCCATTTCCGAGGCTTTGGCTTTGTCAACTTTGAGAAGCATGAG
TAAGCACAGAAGGCTGTGAGTAGCATGAATGGGAAGGAGTTTGGGGTTGTGTCCTGTATGTTGGATAGGCCCAGAAGAAG
ACAGCGAGGCAAAGTGAGCTGAAGCATAGATTTGAGCAGATGAAGCAGGAGAGAGTGAACCGCTACCAGGATATGAATCT
GTATGTGAAGAATCTGGATGATATCATTGATGATGAGAAGTTAAGGAAGGAGTTCTCTCCATATGGCATGATCTCCAGTG
CCAAAGTGATGACAGAGAGTGGCCACAGCAAGGGGTTTGGCTTTGTGTGTTTTTCCTCCCCAGAAGAGGCTACAAAGGCC
ATGACAGAGATGAATGGATGGATTGTTTGCACCAAGCCCCTCTATGTGGCCCTCGCCCAATGCAAGGAAGAGTGGAAGGC
TATCCTCACCAACCAGTACTTGCAACGCATCTCTGTTCTCTGGAACATAAATGGCCCCATCTTTCCCCAACCCACCAATT
ATTTCCTGCCTGCCATCCCCCAGGTGACTGCAATCTTCCAGTCGCCTACC

Alignment

ORF - retro_meug_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 69.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNASGPGYPMASLYVGDLHPDVTEAMLYEKFSAAGPIMSIRVCRDVSTRRSLGYAYINFQQPADAERALD
          MNASGPGYPMASL.VG.LH..V.E.MLYEKFSAAGPIMSIRVC.DV..RRSLGYAYINFQQP...E.ALD
Retrocopy MNASGPGYPMASL*VGNLHSNVNESMLYEKFSAAGPIMSIRVCSDVAMRRSLGYAYINFQQPF--E*ALD

Parental  TMNFEVIKGRPIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFGNILSCKVAYDENGSRGF
          TMNFEVIKGRPI.IMWSQ.DPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTF.NILSCKV..DENG...F
Retrocopy TMNFEVIKGRPICIMWSQQDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFWNILSCKVVCDENGFQEF

Parental  GFVHFETEDAANQAISTMNGMLLNDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQEI
          GFV.F.TED.ANQAISTMNGMLLND.KVF.GHFKS.QE.EA.LGARVLEFTNIYVKNFKENVDDRCLQE.
Retrocopy GFVYFGTEDTANQAISTMNGMLLNDQKVFMGHFKSLQEWEAKLGARVLEFTNIYVKNFKENVDDRCLQEL

Parental  FSQFGKTLSVKVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFG-GRVLYVGRAQKKTERQSELKRR
          FSQFGKTLSVKVMVDENGH.RGFGFVNFEKHE.AQKAVSSMNGKEFG.G.VLYVG.AQKKT.RQSELK.R
Retrocopy FSQFGKTLSVKVMVDENGHFRGFGFVNFEKHE*AQKAVSSMNGKEFG<GCVLYVG*AQKKTARQSELKHR

Parental  FEQMKQERVNRCQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATKA
          FEQMKQERVNR.Q..NLYVKNLDDIIDDEKLRKEFSPYG.I.SAKVMTE.GHSKGFGFVCFSSPEEATKA
Retrocopy FEQMKQERVNRYQDMNLYVKNLDDIIDDEKLRKEFSPYGMISSAKVMTESGHSKGFGFVCFSSPEEATKA

Parental  VTEMNGRIVCTKPLYVALAQRKEERKAILTNQYMQRISVLRNINGPIFPQPTNYFLPAIPQSPTRASFYS
          .TEMNG.IVCTKPLYVALAQ.KEE.KAILTNQY.QRISVL.NINGPIFPQPTNYFLPAIPQ....A.F.S
Retrocopy MTEMNGWIVCTKPLYVALAQCKEEWKAILTNQYLQRISVLWNINGPIFPQPTNYFLPAIPQ--VTAIFQS

Parental  PS
          P.
Retrocopy PT

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_1343 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1343 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,