RetrogeneDB ID: retro_meug_166

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_4957:76721..77363(+)
• Located in intron of: ENSMEUG00000013536

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSMEUG00000007703
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_meug_166
GACTGGCAAGATAGGCATGATGGGTACAGCAATGGGAATCCTCACCTCACTCACCTCCTGGCAGTCAGTCAACACATCTA
TAGTTCAGCAGCCCCACCACTTTCACATTCAGGAGCTTCCAAGTTCCAGCCACCTTACCTCCCACTGTCCTACCATCACT
TACTCTATTCTCAGTCTGCTGACCCGTACTTCCACTTGAGTGACATAGTCTCCATCAACCCCCTGCACCAGCCTGCTCTG
GCAACCAGCCAGCAACAGGCCTAGCCCAGCTGGCAAAACCAGGACCCAGCTGGCCTGAGCAACCACACAAGGCCAGTCCT
TCTCCAGCACCTCTTGAGGCTGGACTCCAGTCCCTCAGGGGCAAAGAGGGAGACTTACAGACATTCTAAGTTGGTCCTGT
AGCCCCACAGCCACCTGCTAGATGCAGTACTGGTAGAAAACCTGGGCTTACATGACATCCATCAAATGGAAGATGTCCAG
AATGTAGAAGACCAACATTAGCTGTTGCGTGATCAGACAGTCATCAGGAAAATTTCTATTTCAATGACCAAAAGCAACTC
CTTGGGTCTCCCCTGTCAGAAAAATGGGATGCTAGGAGCAGTAATCAATCACAATGAACTATTTTGCTCTGCTCCTGGAA
GA

Alignment

ORF - retro_meug_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 70.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DCEDRHDGNSNGNPRLPHLPAVSQHLYSPAAPPLSHSGASDFQPPYFPPPYQPLPYSQSADPYSHLSDPF
          D..DRHDG.SNGNP.L.HL.AVSQH.YS.AAPPLSHSGAS.FQPPY.P..Y..L.YSQSADPY.HLSD..
Retrocopy DWQDRHDGYSNGNPHLTHLLAVSQHIYSSAAPPLSHSGASKFQPPYLPLSYHHLLYSQSADPYFHLSDIV

Parental  AINPLHQPAPATSQQQAWPSRQNQEPAGLSHHTRPGLVPHLSGLDAGAPGTRRETYRRSELLLQPHSHGL
          .INPLHQPA.ATSQQQA.PS.QNQ.PAGLS.HTRP.L..HL..LD....G..RETYR.S.L.L.PHSH.L
Retrocopy SINPLHQPALATSQQQA*PSWQNQDPAGLSNHTRPVLLQHLLRLDSSPSGAKRETYRHSKLVL*PHSHLL

Parental  DAALVENLGLHDMAHQMEDVQNVEDQHLLLHDQTVIRKGPISMTKSNSLGLPCQKDGMLGAVVNHNEVFC
          DA.LVENLGLHD..HQMEDVQNVEDQH.LL.DQTVIRK..ISMTKSNSLGLPCQK.GMLGAV.NHNE.FC
Retrocopy DAVLVENLGLHDI-HQMEDVQNVEDQH*LLRDQTVIRKISISMTKSNSLGLPCQKNGMLGAVINHNELFC

Parental  SVPGR
          S.PGR
Retrocopy SAPGR

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_166 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_166 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166 ,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535,