RetrogeneDB ID: retro_shar_596

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL853944.1:1305..1958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016534
• Aliases: None
• Description: None

Sequence

>retro_shar_596
ATGACCATAGCAGCAAAGCCTACATTTGAATCTGCAAGAGGTAGAAGAGGGAAAGAAGAAGGTGATTTGAGTCCACTTTC
AAAACAATATTCAAGCAGAAATCTACCTTCTCACACAAAGATAAAATACAGACAAACCACTCAGGATGCTCCAGAAGAGG
TTTGCAACTGTGATTTCAGGCAAAAACTAGGAGAGAGAGAGAGAGTTGCTGCAAGAGAGAAAAACAGATAGTGCAACTAG
AGAGCACACAACTTCATCTTCTGTGTCTAAGAAACCTCGGTTAGATCAGATTCATGCAGCCAACCTTGATGCAGATGATC
CCCTAATAGATGAAGACAACAAAGATGAGGATTTTGAGGAAGAAAGTGAAGATGATGACACTGCAACTCTACTGGAAGAA
CTAGAAAAAATAAAAAAAGAGCTGAAGAACAAGCTCTGAAGGAACAAGAACAAAAGGCTGAAGAAGAGAGAATTCGGATG
GAAAATATCCTTCATGGAACCCTCTCCTAAATCTCGCTGGTCCCTCTCAACCTAAGGTCACCTTCAAAGTAAAGAGAAGA
TGGGATGATGTTGTCTTTAAGAACTGAACCAAAGGAGTAGATGAGCTGAAAAAAGACAAAAGATTTGTAAATGATACCCT
TCAATCACAATGG

Alignment

ORF - retro_shar_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 95.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTTAARPTFEPARGGRGKGEGDLSQLSKQYSSRDLPSHTKIKYRQTTQDAPEEVRNRDFRRELEERERVA
          MT.AA.PTFE.ARG.RGK.EGDLS.LSKQYSSR.LPSHTKIKYRQTTQDAPEEV.N.DFR..L.......
Retrocopy MTIAAKPTFESARGRRGKEEGDLSPLSKQYSSRNLPSHTKIKYRQTTQDAPEEVCNCDFRQKLXXXXXXX

Parental  AREKNRDRPTREH-TTSSSVSKKPRLDQIPAANLDADDPLTDEDDEDEDFEEESDDDDTAALLAELEKIK
          ....NR....R.H.T.S.SVSKKPRLDQI.AANLDADDPL.DED..DEDFEEES.DDDTA.LL.EL....
Retrocopy XXXXNR*CN*RAH>TSS-SVSKKPRLDQIHAANLDADDPLIDEDNKDEDFEEESEDDDTATLLEELXXXX

Parental  KE-RAEEQARKEQEQKAEEERIRMENILSG-NPLLNLTGPSQPQANFKVKRRWDDDVVFKNCAKGVDELK
          .E...E.......EQKAEEERIRMENIL.G.NPLLNL.GPSQP...FKVKRRW.DDVVFKN..KGVDELK
Retrocopy XE<AEEQALKEQ-EQKAEEERIRMENILHG<NPLLNLAGPSQPKVTFKVKRRW-DDVVFKN*TKGVDELK

Parental  KDKRFVNDTLRSEF
          KDKRFVNDTL.S..
Retrocopy KDKRFVNDTLQSQW

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_596 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 16 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011392	1 retrocopy	retro_amel_1913,
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Callithrix jacchus	ENSCJAG00000004188	1 retrocopy	retro_cjac_2802,
Cavia porcellus	ENSCPOG00000006249	1 retrocopy	retro_cpor_708,
Dipodomys ordii	ENSDORG00000011075	1 retrocopy	retro_dord_313,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Mus musculus	ENSMUSG00000004096	2 retrocopies	retro_mmus_2482, retro_mmus_593,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Oryctolagus cuniculus	ENSOCUG00000001629	4 retrocopies	retro_ocun_1037, retro_ocun_1605, retro_ocun_679, retro_ocun_743,
Otolemur garnettii	ENSOGAG00000001686	2 retrocopies	retro_ogar_2476, retro_ogar_456,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596 , retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,