RetrogeneDB ID: retro_meug_1016

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold260387:1383..2096(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX7
• Ensembl ID: ENSMEUG00000011320
• Aliases: None
• Description: sorting nexin 7 [Source:HGNC Symbol;Acc:14971]

Sequence

>retro_meug_1016
ATTCATAAGGAAATGATGGAATGGTTTAATGATGACTTCATTGAGACTCAAGGAAAGGCACTGCATAAATTCTTCAATTG
AATTGCTGATCACTCAACTTTAACTTTTAATGAAGACTTCAAAGTTTTTTTTTACTGCACAAGCTGGAAACTCTCTTCTC
ACAAGAGACAAGGTCATGGATTGCTTAACATGATGGGGCAGACAGTGAGAAATGTAGCACCCTCAGTGAGAGCAGTTAAA
AAACTGCCCAGATAAGTTCATTGAAATGAATGATTACGTGGGAACATTTAGTCAGGAGATAAACTTAATAGACAAAATAT
CTGAGAGAATTCACAGGAAAGAAAAGGAGTATTTTGAAGAAATGAAGGAATATGGACCAATCTACACCTGGTGGTATATC
AGAAAATGATCTGGTTGACTCCCTGAAAGATGTGGCCAGCTGAATTTATAAGTGTTATAAAGCCACTGAAAGATGAATAT
TTGATCTTTGAGAGACACTGCTTCCAACTGTATATGAATATGTTCTTTATAGTGAAATATTAATGGGAGTTATGAAAAGA
AGAGACAAAATTCAAGTAGAGCAGGATTCCAGAGTTGAAGCTTTGACCCGCAAAATTGCTGAAAAGGTGTTGCTTACAGA
AGAAATTGGAGAATTAGAAGGTAAGGCAGAATGTGCTAATAATGCTCTGAAAGTGGCATGGAAAACATGCAAA

Alignment

ORF - retro_meug_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 61.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IMKGMVERFNDDFIETRRKALHRFLNRIADHPTLTFNEDFKVFLTAQAWELSSHKKQGPGLLSRMGQTVR
          I.K.M.E.FNDDFIET..KALH.F.N.IADH.TLTFNEDFK.......W.LSSHK.QG.GLL..MGQTVR
Retrocopy IHKEMMEWFNDDFIETQGKALHKFFN*IADHSTLTFNEDFKXXXXCTSWKLSSHKRQGHGLLNMMGQTVR

Parental  AVASSVRGVK-NRPEEFTEMNDYVGTFSQEINLIDKISHRIYKEEKEYFEEMKEYGPIYTWW-SASEEDL
          .VA.SVR.VK.N.P..F.EMNDYVGTFSQEINLIDKIS.RI...EKEYFEEMKEYGPIYT.W...SE.DL
Retrocopy NVAPSVRAVK>NCPDKFIEMNDYVGTFSQEINLIDKISERIHRKEKEYFEEMKEYGPIYT-W>GISENDL

Parental  VDSLKGVASCIDKCCKATERRIFDLSETLLPVVHEYVLYSEILMGVMKRRDQIQAELDSRVEALTYKKTE
          VDSLK.VAS.I.KC.KATER.IFDL.ETLLP.V.EYVLYSEILMGVMKRRD.IQ.E.DSRVEALT.K..E
Retrocopy VDSLKDVAS*IYKCYKATER*IFDL*ETLLPTVYEYVLYSEILMGVMKRRDKIQVEQDSRVEALTRKIAE

Parental  KEVLSEEIGKLEDKVECANNALKADWDRWK
          K..L.EEIG.LE.K.ECANNALK..W...K
Retrocopy KVLLTEEIGELEGKAECANNALKVAWKTCK

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_1016 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1016 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031461	1 retrocopy	retro_btau_453,
Choloepus hoffmanni	ENSCHOG00000008131	2 retrocopies	retro_chof_1097, retro_chof_1388,
Gorilla gorilla	ENSGGOG00000023577	1 retrocopy	retro_ggor_744,
Macropus eugenii	ENSMEUG00000011320	1 retrocopy	retro_meug_1016 ,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420,
Tupaia belangeri	ENSTBEG00000000168	1 retrocopy	retro_tbel_2595,