RetrogeneDB ID: retro_shar_395

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841589.1:2505882..2506148(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL37
• Ensembl ID: ENSSHAG00000013969
• Aliases: None
• Description: ribosomal protein L37 [Source:HGNC Symbol;Acc:10347]

Sequence

>retro_shar_395
GGTAAGAGCCGGAATAAGACACACACTTTGTGCCATCGATATGGTTCTAAGGCGTACCATCTTCACAAGTCATAATGTGG
CAAATGTGATTATGCTGCTAAATGCAAGAGAAAGTATAACTGGAGTGGAAAGGCTAAGCGACGCAACGCCACTGGTACTG
GTTGAATGAGACACTCCAAAATTGTCTGCTGCTGCTTCAGGAATGGATTCTATGAGGGAACAACAGCTAAACCCAAAGAG
CAGCTGCTGCAGCATCTAGTTCATCT

Alignment

ORF - retro_shar_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.89 %
• Parental protein coverage: 91.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYRRFRNGF
          GK.RNKTHTLC.R.GSKAYHL.KS.CGKC.Y.AK.KRKYNWS.KAKRRN.TGTG.MRH.KIV...FRNGF
Retrocopy GKSRNKTHTLCHRYGSKAYHLHKS*CGKCDYAAKCKRKYNWSGKAKRRNATGTG*MRHSKIVCCCFRNGF

Parental  REGTTPKPK-RAAVAASSSS
          .EGTT.KPK.RAA.AASSSS
Retrocopy YEGTTAKPK<RAAAAASSSS

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_395 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 10 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005142	6 retrocopies	retro_btau_1430, retro_btau_1502, retro_btau_1575, retro_btau_1670, retro_btau_181, retro_btau_243,
Callithrix jacchus	ENSCJAG00000007388	10 retrocopies	retro_cjac_107, retro_cjac_1443, retro_cjac_169, retro_cjac_2091, retro_cjac_2443, retro_cjac_247, retro_cjac_2495, retro_cjac_2654, retro_cjac_2956, retro_cjac_332,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Nomascus leucogenys	ENSNLEG00000016508	4 retrocopies	retro_nleu_1841, retro_nleu_2065, retro_nleu_2407, retro_nleu_77,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,
Sarcophilus harrisii	ENSSHAG00000013969	4 retrocopies	retro_shar_295, retro_shar_350, retro_shar_395 , retro_shar_715,