RetrogeneDB ID: retro_meug_1907

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold71182:10782..11786(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF4
• Ensembl ID: ENSMEUG00000003314
• Aliases: None
• Description: TNF receptor-associated factor 4 [Source:HGNC Symbol;Acc:12034]

Sequence

>retro_meug_1907
GAAGGAGTTTTTAAGTGTCCTGAGGATCAGCTACCTTTGGATTGTCATAAGATCTACCCAGACCCAGAACTGGAAGTTCA
GGTGTTCAGTCTAGCTATCCGCTGTATCCACAGTGAGGAGGGCTGCTGCTGGGCAGGAGCCTTACGCCACCTACAGGTCC
ATCTGAGCTCCTGCGGGTACAACGTGGTCTCTTGCCCCAACCAGTGCAGTGCCAAGCTGAGCCGTAGGGACTTCCCTACC
CATCTTCAGCACGAATGCCCCAAGAGGAGGCTCAAGTGTGACTTTCGTGGCACCAACTTTACGGGGGAAGCCTATGAGAG
CCACGAGGGGGTCTGCCCACAAGAGAGCGTGTACTGTGAGAACAAGTGTGGCGCCCGAATGATGCAGCGGCTGCTGGGGC
AACACATGATAGCGGGGTGTTGCAAGCGGACCTAGCCTTGTGCCTATTGCACCAAGGAGTTTGTCTTTAATACGATCCAG
AACCACCAGCACCATTGCCCCGGCTACCCTGTACCGTGCTCCAACCAGTGTGGAATGGGGAGCATTCCTCGAGAGGACTT
GGCTAGCCACCTGAAAGAAAACTGCAGTTCAGCCCCGGTTCTGTGCCCATTCAAAGATGCAGGCTGCAAACACCGGTGCC
CCAAGCTGGCGATGGGCCGCCACATGGAGAAGAGGGTGAAGCCCCACCTGGCCTTGATGTGTGCCCTGGTGAGCCGGCAG
CGGCAGGAGCTGCAGGAGCTGCGAAGTAACGTAGAGGAGCTGTCCGTGGGCTGTGATGTAGTCTTAATCTGGAAGATTGG
CGGCTTTGGGCTCTGCCTTCAGGAAGTCAAGGCTCGCTCCAACCATGAACGCTTCAGCCCAGTCTTCTACACCCACAAGT
ACGGCTACAAGCTCCAGGTGTCGCCTTCCTCAATGGCAACGGCAGTGGGGAGGTGAACCATCTGTCTCTGTACGTCCGGG
TACTGGCCGGAGCCTTTGACAACCTGCTGGAGTGGCCCTTTGCT

Alignment

ORF - retro_meug_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 79.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGVFKCPEDQLPLDYAKIYPDPELEVQVFSLAIRCIHSEEGCRWTGALRHLQVHLSSCGYNVVSCPNRCS
          EGVFKCPEDQLPLD..KIYPDPELEVQVFSLAIRCIHSEEGC.W.GALRHLQVHLSSCGYNVVSCPN.CS
Retrocopy EGVFKCPEDQLPLDCHKIYPDPELEVQVFSLAIRCIHSEEGCCWAGALRHLQVHLSSCGYNVVSCPNQCS

Parental  AKLSRRDLPTHLQHECPKRRLKCDFCGIDFTGEAYESHEGVCPQESVYCENKCGARMMRRLLGQHMIAEC
          AKLSRRD.PTHLQHECPKRRLKCDF.G..FTGEAYESHEGVCPQESVYCENKCGARMM.RLLGQHMIA.C
Retrocopy AKLSRRDFPTHLQHECPKRRLKCDFRGTNFTGEAYESHEGVCPQESVYCENKCGARMMQRLLGQHMIAGC

Parental  PKRTQPCAYCTKEFVFDTIQNHQHQCPRYPVPCPNQCGMGSIPREDLASHLKENCSSAPVLCPFKDAGCK
          .KRT.PCAYCTKEFVF.TIQNHQH.CP.YPVPC.NQCGMGSIPREDLASHLKENCSSAPVLCPFKDAGCK
Retrocopy CKRT*PCAYCTKEFVFNTIQNHQHHCPGYPVPCSNQCGMGSIPREDLASHLKENCSSAPVLCPFKDAGCK

Parental  HRCPKLAMGRHMEDSVKPHLAMMCALVSRQRQELQELRRDVEELSVGCDGVLIWKIGGYGRRLQEAKARS
          HRCPKLAMGRHME..VKPHLA.MCALVSR...........VEELSVGCD.VLIWKIGG.G..LQE.KARS
Retrocopy HRCPKLAMGRHMEKRVKPHLALMCALVSRXXXXXXXXXSNVEELSVGCDVVLIWKIGGFGLCLQEVKARS

Parental  NHECFSPVFYTHKYGYKLQVS-AFLNGNGSGEGTHLSLYIRVLPGAFDNLLEWPFA
          NHE.FSPVFYTHKYGYKLQVS.AFLNGNGSGE..HLSLY.RVL.GAFDNLLEWPFA
Retrocopy NHERFSPVFYTHKYGYKLQVS<AFLNGNGSGEVNHLSLYVRVLAGAFDNLLEWPFA

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_1907 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1907 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003314	1 retrocopy	retro_meug_1907 ,
Ictidomys tridecemlineatus	ENSSTOG00000005085	1 retrocopy	retro_itri_1873,