RetrogeneDB ID: retro_shar_738

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861664.1:298817..299204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSSHAG00000002466
• Aliases: None
• Description: Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592]

Sequence

>retro_shar_738
AGAGAAGACGACTTCGCTCCCAGGGACGACTCGGCCGCCTCTTCGGACTCAGACCAGCTGCGGGTGGGCAACGACGGCAT
CTTCTTGGTGGCCTTCTTCATGGCCTTCATCTTCAACTGGGTCGGCTTTTGCTTATCCTTCTGCACCACCAACTCCATAG
CCGGCAGGTACGGAGCCCTCTGCGGCCTCGGCCTCTCCTTGACCAAGTGGATCCTCATCGTCCGCTTCTCTGACTACTTC
ACTGGATACTTCAATGGACAGTACTGGCTGTGGTGGCTATTCCTCCTGATTGGCCTCCTGCTTTTCTTCAGAGGGTTTTA
CTGTTACCTTAAAGTCAGGAACATGTCTGAAAGGTTGGCCACTGCCAGTAGAACAAGATTTATCTTC

Alignment

ORF - retro_shar_738 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 60.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDDDFVARDDF---DDADQLRIGNDGIFMLTFFMAFLFNWIGFFLSFCLTTSAAGRYGAISGFGLSLIKW
          R.DDF..RDD.....D.DQLR.GNDGIF...FFMAF.FNW.GF.LSFC.T.S.AGRYGA..G.GLSL.KW
Retrocopy REDDFAPRDDSAASSDSDQLRVGNDGIFLVAFFMAFIFNWVGFCLSFCTTNSIAGRYGALCGLGLSLTKW

Parental  ILIVRFSTYFPGYFDGQYWLWWVFLILGFLLFLRGFINYAKVRKMPDTFSTLPRTRVLF
          ILIVRFS.YF.GYF.GQYWLWW.FL..G.LLF.RGF..Y.KVR.M.....T..RTR..F
Retrocopy ILIVRFSDYFTGYFNGQYWLWWLFLLIGLLLFFRGFYCYLKVRNMSERLATASRTRFIF

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_738 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738 ,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,