RetrogeneDB ID: retro_shar_323

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841336.1:21272..21891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000018230
• Aliases: None
• Description: None

Sequence

>retro_shar_323
GAGAATAGTCAAGTGTTGGGAAATGCTGGCTAAGAATTTGATAGCTGCTTTACCTCATTCCAGAAAAGAGCAATCCATAC
CCTTTGGACAGTGCTAGATGCCACCAATAAGATGTAGTGGTCTGTGGTGTGTCTTATGGAGAACTACTATGGGGTTCTGA
CAGACTACAAGAAAGCTGAAATGACTGGTAAATAAGATGAGACTTAGCTGAAGGGGAAGGGAGGCTCCTACAATATCCCA
TCACCTCCAGTAGAGTCCAACTATCCCTTCTATGGTGATATCAGTAAAGATCATTATTATGCAGATCTCTCGAGCACCAA
TTGTTCTGTGAGAGCCTGAAAGACAGACACTATTGCTCAGTCTTTTACCCTTCTGGAATGAGGAAATCATTTCTCAGATC
AAGGAAGGAAAATGTGTTGTAATTGCATTTCATAACAATAACTTTCACCACATTGTGACATATCTTGAGAGTCTGTCTAA
AACCATCAGGAAGCTAAATCTGCCCACTGGCATTTTCCATGTCTATGAATTGGATAAGAAAGTTAAACCCATCCCAGTGT
GATCTCTAAATGATGACAAAACCATGGAGGCTACGGTTGCTTAAGGCAAAACTAAGAAG

Alignment

ORF - retro_shar_323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.78 %
• Parental protein coverage: 89.96 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSSMSLPDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGE
          ..S..L..AG.EFD.CFTS.QKRAI.TLWTVLDA...M...VV....L.E..YG.LT...KAE...K..E
Retrocopy ENSQVLGNAG*EFDSCFTSFQKRAIHTLWTVLDATNKM*WSVVC---LMENYYGVLTDYKKAEMTGK*DE

Parental  AQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARA-LPFWNEEIVPQIKEG
          ...K....SY..P.PP.E...PFY..ISKD..YADL............DTIA...LPFWNEEI..QIKEG
Retrocopy T*LKGKGGSYNIPSPPVESNYPFYGDISKDHYYADLSSTNCSVRA*KTDTIAQS>LPFWNEEIISQIKEG

Parental  KRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAA
          K.V.IA.H.N....IV..LE.LS...I..LNLPTGI..VYELDK..KPI.P...L.D..T....MEA..A
Retrocopy KCVVIAFHNNNFHHIVTYLESLS-KTIRKLNLPTGIFHVYELDKKVKPI-PV*SLNDDKT----MEATVA

Parental  QGKVKK
          .GK.KK
Retrocopy *GKTKK

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_323 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 15 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323 ,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,