RetrogeneDB ID: retro_shar_758

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL862247.1:29030..29915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH7A1
• Ensembl ID: ENSSHAG00000013162
• Aliases: None
• Description: aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:877]

Sequence

>retro_shar_758
CAAAGGCTAAAAGAAGCCTGGGAAATATAAGCAGATACACCAGCTCTTAAACAAGGAGAAATAGTAAACCGCGAAGCCAT
GTGACAGAAGATCCAGATCTTAGGAAATATGGTATCTTTGGAGATGGGAAAAATCTTAGAGGAAGGCACTGCAGAAATTC
AAGAGAATATGGATATCTATGATTATGCTATTGGCTTATCTTGAATGATTGGAGAATCCCTTTTGCCTTATGAAAGATCA
GGGCTCATTGAACAATGGAGTCTTTTGGGCCTAGTTGGGGTCTTCACTGCATACGATTTCCCAGTGGCTGAGTTTGGCTG
GAACAATGCCATTGCTCTGATCTGCAGGGATGTTTGCCTTTGGAAAGGGACACCAATCACTTCTCTCAATAGTACAGCTG
TCAAAAAGATAGTGCCCAAGTTTGGAAGACAATAACCTACCTGGTGTGATTTGTCATATCATATGTGATGGGGCCAATAA
TGGCACGGCAATGGCCAGAGATGAGTGGGTAGACTACTGTCCTTCATGAGAAGGATCCAAGTGGGAAAATAGATGGCAGT
CAGGGTCCAAGAGAGGTTTAAGGAGAAGTTTGTTAGCTTTGGCAGAAATAATGCTATTATTGCGTTGGAGGATACAGACC
TTACTTGGGTTCCCTCAGCTCTCTTTGCAGCTATGGGGACAGAAGTTCAGAGATGTACAACTGCCAGATGATTCTTTTTG
CACGAGAGCATCCATGATGAAGATGTGGATAAACTTAAAAAAGGAATAGCCACATTCCAATTCATATTTATAGATCCATG
GGATCCAAATATTCTCTATGGGTCTCTCTACACCAAAGAGGTAGTAAACATGTTCCTTGGTGCAGTGGAAGGAGCCTAAA
AGCAA

Alignment

ORF - retro_shar_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 55.37 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKAKEAWKIWADIPAPKRGEIVRQIGEALRQKIQILGNLVSLEMGKIFVEGVGEVQEYVDICDYAVGLSR
          ...KEAW.I.AD.PA.K.GEIV....EA..QKIQILGN.VSLEMGKI..EG..E.QE..DI.DYA.GLS.
Retrocopy QRLKEAWEI*ADTPALKQGEIVNR--EAM*QKIQILGNMVSLEMGKILEEGTAEIQENMDIYDYAIGLS*

Parental  MIGGPILPSERPGHALIEQWNPLGLVGIITAFNFPVAVYGWNNAIALIC-GNVCLWKGAPTTSLISVAVT
          MIG...LP.ER.G..LIEQW..LGLVG..TA..FPVA..GWNNAIALIC.G.....KG......I.V...
Retrocopy MIGESLLPYERSG--LIEQWSLLGLVGVFTAYDFPVAEFGWNNAIALIC>GMFAFGKGHQSLLSI-VQLS

Parental  KIVAKVLEENNLPGAICSMTCGGADIGTAMAKDERVD-LLSFTGSTQVGKQVALMVQERFGRSLLELGGN
          K.....LE.NNLPG.IC...C.GA..GTAMA.DE.VD.LLSF....QVGK..A..VQERF.......G.N
Retrocopy KR*CPSLEDNNLPGVICHIICDGANNGTAMARDEWVD<LLSFMRRIQVGK*MAVRVQERFKEKFVSFGRN

Parental  NAIIAFEDADLNLVIPSALFAAVGTAGQRCTTARRLFLHESIHDEVVDKLKKAYA--QIRIGNPWDSNVL
          NAIIA.ED.DL..V.PSALFAA.GT..QRCTTAR..FLHESIHDE.VDKLKK..A..Q.....PWD.N.L
Retrocopy NAIIALEDTDLTWV-PSALFAAMGTEVQRCTTAR*FFLHESIHDEDVDKLKKGIATFQFIFIDPWDPNIL

Parental  YGPLHTKQAVNMFLAAVEDAKKQ
          YG.L.TK..VNMFL.AVE.A.KQ
Retrocopy YGSLYTKEVVNMFLGAVEGA*KQ

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_758 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002143	1 retrocopy	retro_chof_869,
Homo sapiens	ENSG00000164904	1 retrocopy	retro_hsap_3196,
Pongo abelii	ENSPPYG00000025927	1 retrocopy	retro_pabe_2651,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111,
Sarcophilus harrisii	ENSSHAG00000013162	1 retrocopy	retro_shar_758 ,