RetrogeneDB ID: retro_shar_325

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841344.1:429425..430278(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000008496
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSSHAG00000012048
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_shar_325
GCAATGTGTGTTCCTCCATCATATGCTGACCTTGGCAAAGCTGCCAGAGATATTTTCAACAAAGGATTTGGTTTTGGTTT
GGTGAAACTGGATGTGAAAACAAAGTCTTGCAGTGGACTGGAATTCATATCTTTGGGTTCATCTAATACAGACACTGGTA
AAGTTTCTGGGACTTTGGAGACCAAATATAAATGGTGTGAGTATGGTCTGACTTTCACAGAAAAATGGAACACTGATAAC
ACTTTGGGAACCGAAATCGCAATTGAAGACCAGATTTGCCAAGGTTTGAAGCTGACATTTGATACTACCTTCTCACCAAA
CACAGGAAAGAAAAGTGGTAAAAATAAAGTCTTCTTACAAACGAGAATGTATAAACCTTGGCTGTGACATTGATTTTGAT
TTTGCTGTACCTGCCATTCATGGGTCAGCCATTTTTGGTTATGAAGGCTGGCTTGCTGGCTACCAGATGACCTTTGATAG
TGCCAAGTCAAAGTTAACAAGGAATAACTTTGCAGTGGGATACAGGACTGGAGACTTCCAACTGCACACTAATGTCAATG
ATGGAACAGAATTTGGAGGTTCAATTTATCAGAAAGTATGTGAAGATCTTGATATTTCTGTAAACTTAGATTGGACATCA
GACACCAACTGCACTCGTTTTGGAATTGAAGCCAAATATCAATTGGATGAAACTGCTTCTATTTCTGCAAAAGTCAACAA
TTCTAGTTTAATTGGTGTGGGTTATACTCAGACCCTGAGGCCTGGTGTGAAGCTTATGCTGTCTGCCCTGGTGGATGGGA
AAAGCATCAATGCTGGAGGTCACAAACTTGGGCTTGCCTTGGAGTTGGAGGCT

Alignment

ORF - retro_shar_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.79 %
• Parental protein coverage: 96.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMCVPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFTSSGSSNTDTGKVSGTLETKYKWCEYGL
          .MCVPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSG.EF.S.GSSNTDTGKVSGTLETKYKWCEYGL
Retrocopy AMCVPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGLEFISLGSSNTDTGKVSGTLETKYKWCEYGL

Parental  TFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGK-IKSSYKRECINLGCDIDFDFAGPAI
          TFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGK.IKSSYKRECINLGCDIDFDFA.PAI
Retrocopy TFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGK>IKSSYKRECINLGCDIDFDFAVPAI

Parental  HGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNL
          HGSA.FGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLD.SVNL
Retrocopy HGSAIFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDISVNL

Parental  AWTSGTNCTRFGIAAKYQLDETASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKLGLA
          .WTS.TNCTRFGI.AKYQLDETASISAKVNNSSLIGVGYTQTLRPGVKL.LSALVDGKSINAGGHKLGLA
Retrocopy DWTSDTNCTRFGIEAKYQLDETASISAKVNNSSLIGVGYTQTLRPGVKLMLSALVDGKSINAGGHKLGLA

Parental  LELEA
          LELEA
Retrocopy LELEA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_325 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 17 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325 ,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,