RetrogeneDB ID: retro_shar_629

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856832.1:3695738..3695991(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000018506
• Aliases: None
• Description: None

Sequence

>retro_shar_629
TTTGGTATGCAAACTCTAAACATCTGACAGTGGGGCCAAGGAAATAAGATATACGCATGAATGATGGTTTTCTTCCTAAG
GAACACAACTGAAAAGCAGTTATATGTCAATAAGTACTTTTCAGATAAATTTAAATAATGTACCATTCTAGTCAAAGCTA
GCATCTGATCATTTTCCATTCACATAGCAGCTTGTTCAAATTCTTAATGATGAAAAGAAACTCAATGGGCATATGAATTC
AATCCTACATCAT

Alignment

ORF - retro_shar_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.18 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FGMQAPSIWQWGQENKVYACMMVFFLSNMIENQC-MSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILD
          FGMQ...I.QWGQ.NK.YA.MMVFFL.N..E.Q..MS...F.I.LN.VP..SKL.S.H.P...QLVQIL.
Retrocopy FGMQTLNI*QWGQGNKIYA*MMVFFLRNTTEKQL>MSISTFQINLNNVPF*SKLASDHFPFT*QLVQILN

Parental  NEMKLNVHMDSIPHH
          .E.KLN.HM.SI.HH
Retrocopy DEKKLNGHMNSILHH

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_629 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629 ,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,