RetrogeneDB ID: retro_meug_1274

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold34874:11416..12645(-)
• 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_1274
ATGAACGCAAGTTGCCCTGGCTACCCCATGGTGTCCTTCTACATGGGCGACCTGCAACCCAATGTGACTGAGGCCATACT
GTACGAGAAGTTCTTGGCCACAGGGCCCATCATGTCCATCCGTGTGTACTGTGATGTGGCTACATGCAGCTCCCTCGGTT
ATGCCTACATCAACTTCCAGCAGCGTGCAGACACTGAATGAGCCTTGGACACCATGACCTTTGAGGTAATCAAGGGCAGG
CCCATCCATATCATGTGGTCCCAGGGGGATATGGGGCTCTGGAAATCAGGAATTGGCAATATCTTTATCAAGAACTTGAA
TGATTCCATTGACAACAAGGCCTTATATGACACTTTTTATACCTTTGGGAACATCCTCACTTGCAAGGTGGTGTGTGATG
AGAATGGCTCCCGAGGATTTGGTTTTGTCCACTTTGAGACCAAGGATGCTGCAAACCAAGCAATCAGCACTGTGAATGGA
ATGCTACTAATGACTGGAAAGTTTTCATGGGCCACTTCAAGTCTCAGCAGGAATGGGAGTCAGAACTGGGGGCATGAGTG
TTGAGCTTCACCAACATCTACATCAAGACCTTCAAGGAAAACCTGGATGATCAGTGCCTTCAGGAACTCTTCTCCCAGTT
TGGAAAGACTCTAAGTGTTAAGGTGATGGTTGATGAAAATGGCCGTTCCTGAGGATTTGGCTTTGTCAACTTTGAGAAGC
ATGAAGAAGCACAGAAGGCTGTGAGTAGCATGAATGGGAAGGAACTCAGGGGTCATTTCCTATATGTTGGATGAGCCCAG
AAGAAGACAGAGAGACAGAGTGAGCTGAAGCATAGATTTGAGCAGATGAATCAGGAGAGAGTGAACTACTACCAGGGTGC
GAATCTGTATGTGAACAATCTGGATGACGTCACTGATGATGAGATGCTAAGGAAGGAGTTCTCTCAGTATGGCATGATCA
CCAGTGCCAAAGTGATGACAGAGGGTGGCCACAGCAAGGGGTTTGATTTTCTGTGTTTGTCCTCCCCAGACAAGGCTACA
AAGATCATGACAGAGATGAACGGGAAGATTGTTTGCACCAAGTCCCTCTATGTGGCCCTCACCCAATGCAAGGAAGATTG
GAAGACCATACTCACCAACGAGTACTTGCAAAGCATCTCTGTCCTCTGGAATATAAAGAGCCCCATATTTCCCCAACCCA
CCAATTATTTCTTGCTTGCCATTCCACAG

Alignment

ORF - retro_meug_1274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.29 %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNASGPGYPMASLYVGDLHPDVTEAMLYEKFSAAGPIMSIRVCRDVSTRRSLGYAYINFQQPADAERALD
          MNAS.PGYPM.S.Y.GDL.P.VTEA.LYEKF.A.GPIMSIRV..DV.T..SLGYAYINFQQ.AD.E.ALD
Retrocopy MNASCPGYPMVSFYMGDLQPNVTEAILYEKFLATGPIMSIRVYCDVATCSSLGYAYINFQQRADTE*ALD

Parental  TMNFEVIKGRPIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNKALYDTFSTFGNILSCKVAYDENGSRGF
          TM.FEVIKGRPI.IMWSQ.D.GL.KSGIGNIFIKNL.DSIDNKALYDTF.TFGNIL.CKV..DENGSRGF
Retrocopy TMTFEVIKGRPIHIMWSQGDMGLWKSGIGNIFIKNLNDSIDNKALYDTFYTFGNILTCKVVCDENGSRGF

Parental  GFVHFETEDAANQAISTMNGMLL-NDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQE
          GFVHFET.DAANQAIST.NGMLL.ND.KVF.GHFKS.QE.E.ELGA.VL.FTNIY.K.FKEN.DD.CLQE
Retrocopy GFVHFETKDAANQAISTVNGMLL<NDWKVFMGHFKSQQEWESELGA*VLSFTNIYIKTFKENLDDQCLQE

Parental  IFSQFGKTLSVKVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFGGRVLYVGRAQKKTERQSELKRR
          .FSQFGKTLSVKVMVDENG.S.GFGFVNFEKHEEAQKAVSSMNGKE..G..LYVG.AQKKTERQSELK.R
Retrocopy LFSQFGKTLSVKVMVDENGRS*GFGFVNFEKHEEAQKAVSSMNGKELRGHFLYVG*AQKKTERQSELKHR

Parental  FEQMKQERVNRCQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATKA
          FEQM.QERVN..QG.NLYV.NLDD..DDE.LRKEFS.YG.ITSAKVMTEGGHSKGF.F.C.SSP..ATK.
Retrocopy FEQMNQERVNYYQGANLYVNNLDDVTDDEMLRKEFSQYGMITSAKVMTEGGHSKGFDFLCLSSPDKATKI

Parental  VTEMNGRIVCTKPLYVALAQRKEERKAILTNQYMQRISVLRNINGPIFPQPTNYFLPAIPQ
          .TEMNG.IVCTK.LYVAL.Q.KE..K.ILTN.Y.Q.ISVL.NI..PIFPQPTNYFL.AIPQ
Retrocopy MTEMNGKIVCTKSLYVALTQCKEDWKTILTNEYLQSISVLWNIKSPIFPQPTNYFLLAIPQ

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_1274 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1274 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,