RetrogeneDB ID: retro_shar_631

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856857.1:11159..11913(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011828
• Aliases: None
• Description: None

Sequence

>retro_shar_631
CAAGTTATACAGAAGTATTATACATTGCCATGGACACCTAGTTTCCAGGTGTGGCTGCAAGACTCACTGGAGAATTCAGA
AGTAATGCCAGTACCAACTATTGAGATGTAATGTAGATTTGCTAAAGATAATTCAGCTTGGGTTAACATATGAGCAAGGA
GAATACTCTGCAGAAACTTCAACACAGCAGTTCAATTTCAAATTTAATTCAATGGTTGACATGTATGCTCAGGACTCCAT
AGAGTTCCTAATAACCTCTGGGATCTAGTTTAAAAAGTATGAGGAAGAAGGGATTGAGACACAGTATTTTGCAGAACTTC
ACATGACATCAGGTGTCATGTTGTCTAAGGGAGTCAAGTGGTTTTCATTTCACAGTGTTCATGACTTTGGCTATTTAGTC
AAAATCCTGACCAATTCTAATTTGCCTGAAGAAGAACTGGACTTCCTTGAAATCCTCCGATTTTTTTTTCTGGTCATCTA
CAATATTAAGTACCTCATGAAGAATTGCAAAAACCTCAAGGGTGGCTTACAGGAAGTGGCTGAGCAGCTGGAGTAGGAGC
GGATAGGACCACAGCACCAGGCAGGATCTTACTCATTACTGACAGGAATGGCCTTTTTCAAAATGAGAGAAATGTTCTTT
GAAGATCACATCCATGATGCCAAGTATTGTGGACACTTATACCTCTTTGATTCGGGCTTCTCCTGTGTGCAGAACAATAT
GGGGAATGTGCATGAAGAGGAAGCCAGCAAGCAG

Alignment

ORF - retro_shar_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 89.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVIRKYN-YVAMDTEFPGVVARPIGEFRSNA-DYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQ
          QVI.KY..Y.AMDT.FPGV.AR..GEFRSNA..YQ..LLRCNVDLLKIIQLGLT...EQGEY...TST.Q
Retrocopy QVIQKYY<YIAMDT*FPGVAARLTGEFRSNA<QYQ--LLRCNVDLLKIIQLGLTY--EQGEYSAETSTQQ

Parental  FNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLI
          FNFKFN...DMYAQDSIE.L.TSGI.FKK.EEEGIETQYFAEL.MTSGV.L..GVKW.SFHS..DFGYL.
Retrocopy FNFKFNSMVDMYAQDSIEFLITSGI*FKKYEEEGIETQYFAELHMTSGVMLSKGVKWFSFHSVHDFGYLV

Parental  KILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGM
          KILTNSNLPEEELDF.EILR....VIY..KYLMK.CKNLKGGLQEVAEQLE.ERIGPQHQAGS.SLLTGM
Retrocopy KILTNSNLPEEELDFLEILRXXXLVIYNIKYLMKNCKNLKGGLQEVAEQLE*ERIGPQHQAGSYSLLTGM

Parental  AFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEEASKQ
          AFFKMREMFFEDHI.DAKYCGHLY...SG.S.VQN..GN..EEEASKQ
Retrocopy AFFKMREMFFEDHIHDAKYCGHLYLFDSGFSCVQNNMGNVHEEEASKQ

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_631 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Gorilla gorilla	ENSGGOG00000015762	2 retrocopies	retro_ggor_282, retro_ggor_3027,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Monodelphis domestica	ENSMODG00000019055	2 retrocopies	retro_mdom_1898, retro_mdom_802,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631 ,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,