RetrogeneDB ID: retro_meug_67

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_1127:31877..32762(-)
• Located in intron of: ENSMEUG00000010414

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSMEUG00000006710
• Aliases: None
• Description: polypyrimidine tract binding protein 1 [Source:HGNC Symbol;Acc:9583]

Sequence

>retro_meug_67
AATGGAAATGACAGCAAGAAATTCAAAGGTGATAACAGAAGCACAGGAGTCCCTTCCCGAGTAATCCATGTGAGAAAACT
CCCAGGTGACGTCACAGAAGCTGAGGTTATTTCCCTGGGATTACCATTTGGCAAGGTCACCAATCTTCTAATGCTGAAAG
GCAAAAACCAGGCTTTCCTTGAAATGAACACAGAAGAGGCATCAAACACTATGGTAAGTTACTATACCACAGTGACTCCT
GTCCTCCGAAGCCAGCCTATCTACATTCAGTTCTCAAACCACAAGGAGCTGAAAACAGACAACTCTCCAAACCAAGCACG
TGCCCAGGCAGCACTTCAAGCTGTAAACTCTGTTCAGTCAGGAAATTTGGCCCTCTCTGCCTCTGCTGCAGCAGCCGATG
CAGGAATGGCAGTGGCTGGCCAGAGTCCAGTTTTGAGGATCATCGTAGAAAATCTCTTCTACCCAGACACTTTAGATGTG
CTTCACCAGATTTTCTCCAAGTTTGGCACAGTACTGAAAATAATAACCTTCACCAAGAACAACCAGTTCCATTCTCTGTT
ACAATATTCTAACGCTGTGAGTGCCCAGCACGCTAAGTTGTCTCTTGATGGGCAGAATATCTACAATGCTTGTTGTACAC
TGCGCATTGATTTCTCTAAACTCACCAGCCTCAATGTGAAATACAACAATGATAAAAGCAGAGACTATACCCGCCCAGAT
CTGCCCTCTGGTGACAGCCAGCCTTTTCTTGACCAGACTATGGCAGCAGCCTTTGGACTCTCCGTTCCAAATGTTCATGG
AGCTCTTGCTCCACTGGCGATTCCATCATCAGCTGCTGCTGCTGCTGCAGCCGGGCGAATTGCCATCCCTGGCCTCACAG
GGGCA

Alignment

ORF - retro_meug_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGNDSKKFKGDNRSTGVPSRVIHVRKLPGDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTEEASNT
          NGNDSKKFKGDNRSTGVPSRVIHVRKLPGDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTEEASNT
Retrocopy NGNDSKKFKGDNRSTGVPSRVIHVRKLPGDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTEEASNT

Parental  MVSYYTTVTPVLRSQPIYIQFSNHKELKTDNSPNQARAQAALQAVNSVQSGNLALSASAAAADAGMAVAG
          MVSYYTTVTPVLRSQPIYIQFSNHKELKTDNSPNQARAQAALQAVNSVQSGNLALSASAAAADAGMAVAG
Retrocopy MVSYYTTVTPVLRSQPIYIQFSNHKELKTDNSPNQARAQAALQAVNSVQSGNLALSASAAAADAGMAVAG

Parental  QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYSDPVSAQHAKLSLDGQNIYNA
          QSPVLRIIVENLFYP.TLDVLHQIFSKFGTVLKIITFTKNNQF..LLQYS..VSAQHAKLSLDGQNIYNA
Retrocopy QSPVLRIIVENLFYPDTLDVLHQIFSKFGTVLKIITFTKNNQFHSLLQYSNAVSAQHAKLSLDGQNIYNA

Parental  CCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGAPGIISASPYAGAGFPPTFAI
          CCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQP.LDQTMAAAFG..........A....P...A.
Retrocopy CCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPFLDQTMAAAFGLSVPNVHGALAPLAIPSSAAA

Parental  PQAAG-LSVPNVHGA
          ..AAG....P...GA
Retrocopy AAAAGRIAIPGLTGA

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_67 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_67 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 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67 ,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,