RetrogeneDB ID: retro_shar_490

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849679.1:3261660..3262137(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSSHAG00000007465
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_shar_490
GTTTCTGACCTGATGAGTATAGAAAAGATTGTATTTAAGAAGGTGTGCTGGAAAATCAAAGCTACTACTGCCTTTCATTT
TCTACAGCTCTATTAGTCAACATGAAAACTTACTGGTCAAAAGTAGAAAGAACCTGAATTTTAAAAGACTGGAAGCTTAG
CTTAAGGCTAATATTAGGATTATGTTTTCTAAAGCAAAACCTTCTCTATTGGCATTGTCTATAATTGCACTGGAACTTCA
AGCACAGGAAATTTATAGAATTGACAGAAGAAGTAGAATGTCTTCAGAACATTCCAAAATAAATTGCAAAGATCTGATCA
TCTGGCAGAAATTTATAGTAAAATCCCTAACTGAATACGTATCTAACAAGTGTTTTAAACCAAATGTTCATAAGTTAAGG
TGGAGTGCTATATAGGTGTACTGCAAATCACTTGATCATATTCATTACAAATCTCTCATTTTCCAACAATTCCAGAA

Alignment

ORF - retro_shar_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.52 %
• Parental protein coverage: 54.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VSDLMRMEK-IVLEKVCWKVKATTAFQFLQLYYSLI--HENLPFERRKNLSFERLEAQLKACHCRIMFSK
          VSDLM..EK...L.....K.K....F......YS.I..HENL....RKNL.F.RLEA.LKA...RIMFSK
Retrocopy VSDLMSIEK>LYLRRCAGKSKLLLPF----IFYSSISQHENLLVKSRKNLNFKRLEA*LKA-NIRIMFSK

Parental  AKPSVLALSIIALEIQAQ-KFIELTEGVECLQ-KHSKINGRDLTFWQELVAKCLTEYSSNKCSKPNVQKL
          AKPS.LALSIIALE.QAQ.KFIELTE.VECLQ..HSKIN..DL..WQ....K.LTEY.SNKC.KPNV.KL
Retrocopy AKPSLLALSIIALELQAQ>KFIELTEEVECLQ<EHSKINCKDLIIWQKFIVKSLTEYVSNKCFKPNVHKL

Parental  KWIVSGRTARQLKHSYYK-IAHLPTIPE
          .W.........L.H..YK.I.H.PTIPE
Retrocopy RWSAI*VYCKSLDHIHYK<ISHFPTIPE

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_490 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 17 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490 ,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,