RetrogeneDB ID: retro_tsyr_544

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_137464:1..679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSTSYG00000011937
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773]

Sequence

>retro_tsyr_544
GACGTCTGTGCCACCTCCCGAACCGACCGGGAGATCAAGGTAACCCTGGTGTTTGAGCATATAGACCAAGACCTAAGGAC
ATACCTGGATAAGCCACCCCCGCCAGGCTTGCCAGTGGAGACCATCAAGGATCTGATGCGCCAGTTTCTAAGAGGCCTGG
ATTTCCTTCATGCCAATTGCATCGTTCACCGAGATCTGAAGCCAGACAACATTCTGGTGACAAGCAGTAGGACAGTCAAG
CTGGCTGACTTTGGCCTGGCCAGAGTCTACAGCTACCAGATGGCGCTTACACCTGTGGTTGTCACACTCTGGTATTGAGC
TCCCGAAGTGCTTCTGCAGTCGACATACGCAACACCTGTCGACATGTGGAGCGTTGACTGTATCTTTGCAGAGATGTTTC
GGCGAAAGCCTCTTTTCTGTGGAAACTCTGAAGCCGACCAGTTGGGCAAAATCTTTGACCTGATTGGGCTCCCTCCAGAG
GATGACTGGCCCCAAGATGTGTCTGCCGCGGGGAGCCTTCCCCCCAGGGGCCCCGCCGTGCAGTCAGTGGTGCCTGAGAT
GGAGGCGCCTGGAGCACAGCTTCTGCTGGAGATGCTGACTTTTAACCCACACAAGCGAACCTCTGCCTTCCGAGCGCTGC
AGCACGCCTATCTGCATAAGCATGAAGGTACTCCGGAG

Alignment

ORF - retro_tsyr_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.23 %
• Parental protein coverage: 75.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVCATSRTDREIKVTLVFEHIDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCIVHRDLKPEN
          DVCATSRTDREIKVTLVFEHIDQDLRTYLDK.PPPGLPVETIKDLMRQFLRGLDFLHANCIVHRDLKP.N
Retrocopy DVCATSRTDREIKVTLVFEHIDQDLRTYLDKPPPPGLPVETIKDLMRQFLRGLDFLHANCIVHRDLKPDN

Parental  ILVTSSGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFC
          ILVTSS.TVKLADFGLAR.YSYQMALTPVVVTLWY.APEVLLQSTYATPVDMWSV.CIFAEMFRRKPLFC
Retrocopy ILVTSSRTVKLADFGLARVYSYQMALTPVVVTLWY*APEVLLQSTYATPVDMWSVDCIFAEMFRRKPLFC

Parental  GNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRIS
          GNSEADQLGKIFDLIGLPPEDDWP.DVS...G..PPRGP..VQSVVPEME..GAQLLLEMLTFNPHKR.S
Retrocopy GNSEADQLGKIFDLIGLPPEDDWPQDVS-AAGSLPPRGP-AVQSVVPEMEAPGAQLLLEMLTFNPHKRTS

Parental  AFRALQHSYLHKDEGNPE
          AFRALQH.YLHK.EG.PE
Retrocopy AFRALQHAYLHKHEGTPE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_544 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544 ,