RetrogeneDB ID: retro_shar_295

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841248.1:793921..794134(-)
• 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_295
TATCATCTTCAGAAGTCAACATAAGGCAAATTTGTATACAAAGTTAGACATAAGAGAAAAAAACAACTACATTGCTAAGG
CAAAGAGATACAGCATATTGGTTCTGGTTAAATAAGGCACCTAAAAATTGTCTCCTCCCAATTCAGAAATGGATTACATG
AAGGAGCAAAGCCTAAAACTCAAGAAGTAGCTATCAGAAAATCTAGTTCATCT

Alignment

ORF - retro_shar_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.79 %
• Parental protein coverage: 73.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YHLQKSTCGKCGYPAKRKR-KYNWSAKAKRRNT-TGTGRMRHLKIVYRRFRNGFREGTTPKPKRAAVAAS
          YHLQKST.GK..Y....KR.K.N..AKAKR.....G.G..RHLKIV...FRNG..EG..PK....A...S
Retrocopy YHLQKST*GKFVYKVRHKR>KNNYIAKAKRYSI<IGSG*IRHLKIVSSQFRNGLHEGAKPKTQEVAIRKS

Parental  SSS
          SSS
Retrocopy SSS

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_295 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,