RetrogeneDB ID: retro_shar_558

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849907.1:2338366..2338794(+)
• Located in intron of: ENSSHAG00000016738

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSSHAG00000013568
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_shar_558
TATGGCTACATTAAGGTGTCATAAAGGACATAATCTATGATCTAGGCTGAAGGGTTTCTCTAGCAAAGGTACATTGCTGG
GATCCTTACTGATTTAAAAAGAAGACAAAGTTGTTCATTGCTGCTGAAGGTATCCATATGGACTAGTTTGTGTACTGTGG
TAAGAAACTTCAGCTCAACATTAGCAATATCCTGTCAATTGGTACTATGCCTGAAAGGACCATAGTTTGCTGTCTTGAAG
AAAAGCCTGTTGACCAGGATAAGTTTGCCCAAGCATCTGGAAACTAAGCCACAGTGATTTCCCACAATCTGAAACCAAGA
AAACATGCCTGAAAGCTACCTTCAGGCTCAAAGAAAGTGATCCCTGCAAACACAGCTGTGGTTAGTGTTGTTTCTGGAGG
AGATCATACTAATAAACTCATCCTTAAG

Alignment

ORF - retro_shar_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.9 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HGYIK-GIVKDIIHDPGRGAPLAKVAFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGT
          .GYIK.G..KDII.D.G....LAKV...DPY.FKK.T.LFIAAEGIH...FVYCGKK.QLNI.N.L..GT
Retrocopy YGYIK<GVIKDIIYDLG*RVSLAKVHCWDPY*FKKKTKLFIAAEGIHMD*FVYCGKKLQLNISNILSIGT

Parental  MPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRID
          MPE.TIVCCLEEKP.D..K.A.ASGN.ATVISHN....K...KLPSGSKKVI..AN.AVV.VV.GG....
Retrocopy MPERTIVCCLEEKPVDQDKFAQASGN*ATVISHNLKPRKHA*KLPSGSKKVI-PANTAVVSVVSGGDHTN

Parental  KPILK
          K.ILK
Retrocopy KLILK

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_558 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Macropus eugenii	ENSMEUG00000013824	9 retrocopies	retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica	ENSMODG00000004283	3 retrocopies	retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Sarcophilus harrisii	ENSSHAG00000013568	2 retrocopies	retro_shar_482, retro_shar_558 ,