RetrogeneDB ID: retro_meug_475

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold11994:364..1525(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSMEUG00000009110
• Aliases: None
• Description: sorting nexin 5 [Source:HGNC Symbol;Acc:14969]

Sequence

>retro_meug_475
ATGGCCTCCGTTCCCGAGCTGCTGAAGCAGGAAGACGACCGCAGCAAGATGAGATCTGTGTCTGTGGACCTGAATGTTGA
TCCTTCACTCCTGATTGACATCCCTGATGCCCTCAGTGAAAGAGATAAGGTCAAGTTCACAGTGCATACAAAGACCACCC
TGTCCATTTTTCAGAGTCCAGAGTTTTCTGTTACAAGACAGCATGAAGATTTTGTGTGGCTACATGATACACTTACAGAA
ACTGAAGAATATGCAGGACTCATTATACCACCTGCTCCTACAAAGCCTGACTTTGATGGCCCCAGAGAGAAGATGCAGAA
GCTGGGAGAAGGTGAAGGCTCTATGACAAAAGAAGAATTTGCAAAAATGAAGCAAGAACTCGAAGCGGAATATCTAGCTG
TCTTTAAGAAGACTGTATCATCCCATGAAGTTTTTCTTCAGCGACTTTCTTCTCATCCTGTCCTCAGCAAAGATCGCAAC
TTTCATGTTTTCCTGGAATATGATCAGAATCTAAGTGTTAGGAGGAAAAACACTAAGGAGATGTTTGGTGGCTTCTTTAA
GAGTGTGGTGAAAAGTGCTGATGAAGTTCTTTTTTCTGGAGTTAAGGAAGTAGATGACTTCTTTGACCAAGAGAAGAATT
TCCTCATCAACTATTACAATAGGATCAAGGATTCATGTGCAAAAGCCGACAGAATGACCAGATCTCATAAAAATGTCGCA
GATGATTATATCCATACTTCAGCCTGCTTGAATAGCCTCGCTTTAGAAGAGCCAACTGTCATCAAAAAATATTTACTGAA
AGTTGCTGAGCTATTTGAAAAGCTAAGAAAAGTGGAGGGTCGAGTATCATCAGATGAAGATTTAAAACTGACAGAGCTCC
TCAGATATTATATGCTCAACATAGAAGCTGCTAAGGATCTTTTGTACAGACGTACAAAAGCCCTCATTGACTATGAAAAC
TCAAACAAAGCTCTGGACAAAGCCCGGTTAAAAAGCAAAGATGTCAAATTGGCTGAGGCACACCAGCAAGAATGCTGTCA
GAAATTTGAGCAGCTCTCTGAATCTGCGAAAGAAGAACTGATCAGTTTTAAACGGAAAAGAGTGGCAGCATTTAGGAAAA
ACCTAATTGAAATGTCTGAACTGGAAATAAAGCATGCAAAA

Alignment

ORF - retro_meug_475 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVPELLKQEDDRSKMRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLSIFQSPEFSVTRQHED
          MASVPELLKQEDDRSKMRSVSVDLNVDPSL.IDIPDALSERDKVKFTVHTKTTLSIFQSPEFSVTRQHED
Retrocopy MASVPELLKQEDDRSKMRSVSVDLNVDPSLLIDIPDALSERDKVKFTVHTKTTLSIFQSPEFSVTRQHED

Parental  FVWLHDTLTETEEYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVS
          FVWLHDTLTETEEYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVS
Retrocopy FVWLHDTLTETEEYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVS

Parental  SHEVFLQRLSSHPVLSKDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFDQ
          SHEVFLQRLSSHPVLSKDRNFHVFLEYDQ.LSVRRKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFDQ
Retrocopy SHEVFLQRLSSHPVLSKDRNFHVFLEYDQNLSVRRKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFDQ

Parental  EKNFLINYYNRIKDSCAKADRMTRSHKNVADDYIHTSACLNSLALEEPTVIKKYLLKVAELFEKLRKVEG
          EKNFLINYYNRIKDSCAKADRMTRSHKNVADDYIHTSACLNSLALEEPTVIKKYLLKVAELFEKLRKVEG
Retrocopy EKNFLINYYNRIKDSCAKADRMTRSHKNVADDYIHTSACLNSLALEEPTVIKKYLLKVAELFEKLRKVEG

Parental  RVSSDEDLKLTELLRYYMLNIEAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFE
          RVSSDEDLKLTELLRYYMLNIEAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFE
Retrocopy RVSSDEDLKLTELLRYYMLNIEAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFE

Parental  QLSESAKEELISFKRKRVAAFRKNLIEMSELEIKHAK
          QLSESAKEELISFKRKRVAAFRKNLIEMSELEIKHAK
Retrocopy QLSESAKEELISFKRKRVAAFRKNLIEMSELEIKHAK

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_475 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_475 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475 ,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,