RetrogeneDB ID: retro_hsap_1598

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:76552266..76554031(-)
• Located in intron of: ENSG00000140374

Retrocopy information

• Ensembl ID: ENSG00000259581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TYRO3
• Ensembl ID: ENSG00000092445
• Aliases: TYRO3, BYK, Dtk, RSE, Sky, Tif
• Description: TYRO3 protein tyrosine kinase [Source:HGNC Symbol;Acc:12446]

Sequence

>retro_hsap_1598
ATGGTGCTGAGGCACAGCATGGGGCGGCTGGGGCTCCTGCTGCTGCCGCCACAGCAGCTGGGGCTGCTGCTGGCGGCTCT
GACTTCTCTGCTGCTCCCAGAGTCCGCAGCTGCAGGCAGGTCTGAAGCTCGTGGGAGTCCCGGCAAAGCTGACAGTGTCC
CAGGGGCAGCTGGTAAAGCTCAGCTGCAGCATGGAGGGGATGGAGGAGCCTGACATCCAGTGGGTGAAGGATGGGTCTGT
GGTCCAGAACTGGTTCATCCCAGTCAGCGAGCAGCACTGGATCGGCTTCCTCAGCCTGAAGTCAGTGGAGCGCTCTGACA
CGGGCCAGTACTGGTGCAAGGTGGATGGGGGCGAAACCCAGATCTCCCAGCCAGTGTGGCTCACGGTAGTAGGTGTGCCA
CTTTTCACAGTGGAGCCAAAAGATCTGGCAGTGCCACCCAATGCCCCTTTCCAACTGTCTTGCAAGGCTGTGGGTCCCCC
TGAACCTGTTACCATTGTCTGGTGGAGAGGAACTACGAAGATCGGGGGACCTGCTCCCTCTCCATTTGTTTTAAATGTAA
CAGGGGTGACCCAGAGCACCCATGTTTTCCTGTGAAGTTCACAGCCTAAAATGCCTGGCCTCTTCTCGCATAGCCACTGT
TCTCCTTCAAGCACTGCCTGCAGTCCCCTTCAACATCACCGTGACAAAGCTTTCCAGCGGCAACACTAGTGTGGCCTGGA
TGCCAGGTGCTGATGGCCGAGCCCTGCTGCAGTCCTGTACAGTTCAGGTGACACAGGCCCCAGGAGGCTGGGAAGTCCTG
GCTGTTGTGGTCCTTGTGCCCCCCTTTACCTGCCTGCTCCGGGACCTGGTGCCTGCCACCAGCTACAGCCTCAGGGTGTG
CTGTGCCAATGCTTTGGGGCCCTCTCCTTATGCTGACTGGGTGCCCTTTCAGACCAAGGGTCTAGCCCCAGCCAGCGCTC
CCCAAAACCTCCATGCCATCCACACAGATTCAGGCCTCATCTTGGAGTGGGAAGAAGTGATCCCCGAGGGCCCTTTGGAA
GGCCCCCTGGGACCCTATAAACTGTCCTGGGTTTAAGACAATGGAACCCAGGATGAGCTGACAATGGAGGGGACCAGGGC
CAATTTGACAGGCTGGGATCCCCAAAAGGGCCTGATCGTACGTGTGTGTGTCTCCAGTGCAGTTGGCTGTGGACCCTGGA
GTCAGCCACTGGTGGTCTCTTCTCATGACCATGCAGGCCAGAAGGGCCCTCCTCACAGCCGCACATCCTGGGTACCTGTG
GTCCTTGGTGTGCTAACGGCCCTGGTGACGGCTGCTGCCCTGGCCCTCATCTTGCTTCAAAAGAGACCGAAAGAGACGTG
GTTTGGGCAAGGCTTTGACAGTGTCATTTCCCGGGGAGAGCCAGCCATTCACTTCTGGGCAGCCCGGTCCTTCAATCAAG
AAAGGCCCAAGTGCATCGAGGCCACATTGGAAAGCTTGGGCATCAACAGCGAACTAAAGGAAAAACTGGAGGATGTGCTC
ATCCCAGAGCAGCAGTTCACCCTGGCTGGATATAGGGCAAAGGAGAGTTTGGTTCAGTGCGGTAGGCCCAGCTGAAGCAG
GAGGATGGCTCCTTTGTGAAAGTGGCTATGAAGATGCTGAAAGCTGATCTCATTGCCTCAAGTGACATTGAAGAGTTCCT
CAGGAAAGCAGCTTGCATGAAGGAGTTTGACCATCCACATGTGGCCAAACTTGTTGGGGTAAGCCTCTGAGCCTCTGGAG
CAGGG

Alignment

ORF - retro_hsap_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.45 %
• Parental protein coverage: 66.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALRRSMGRPGLPPLPLPPPPRLGLLLAALASLLLPES-AA-AGLKLMGAPVKLTVSQGQPVKLNCSVEG
          M.LR.SMGR.G...L.L.PP..LGLLLAAL.SLLLPES.AA.AGLKL.G.P.KLTVSQGQ.VKL.CS.EG
Retrocopy MVLRHSMGRLG---LLLLPPQQLGLLLAALTSLLLPESAAA>AGLKLVGVPAKLTVSQGQLVKLSCSMEG

Parental  MEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLSLKSVERSDAGRYWCQVEDGGETEISQPVWLTVEGV
          MEEPDIQWVKDG.VVQN.....IPVSEQHWIGFLSLKSVERSD.G.YWC.V.DGGET.ISQPVWLTV.GV
Retrocopy MEEPDIQWVKDGSVVQNW---FIPVSEQHWIGFLSLKSVERSDTGQYWCKV-DGGETQISQPVWLTVVGV

Parental  PFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQST-MFSCEAHN
          P.FTVEPKDLAVPPNAPFQLSC.AVGPPEPVTIVWWRGTTKIGGPAPSP.VLNVTGVTQST.MFSCE.H.
Retrocopy PLFTVEPKDLAVPPNAPFQLSCKAVGPPEPVTIVWWRGTTKIGGPAPSPFVLNVTGVTQST>MFSCEVHS

Parental  LKGLASSRTATVHLQALPAAPFNITVTKLSSSNASVAWMPGADGRALLQSCTVQVTQAPGGWEVLAVVVP
          LK.LASSR.ATV.LQALPA.PFNITVTKLSS.N.SVAWMPGADGRALLQSCTVQVTQAPGGWEVLAVVV.
Retrocopy LKCLASSRIATVLLQALPAVPFNITVTKLSSGNTSVAWMPGADGRALLQSCTVQVTQAPGGWEVLAVVVL

Parental  VPPFTCLLRDLVPATNYSLRVRCANALGPSPYADWVPFQTKGLAPASAPQNLHAIRTDSGLILEWEEVIP
          VPPFTCLLRDLVPAT.YSLRV.CANALGPSPYADWVPFQTKGLAPASAPQNLHAI.TDSGLILEWEEVIP
Retrocopy VPPFTCLLRDLVPATSYSLRVCCANALGPSPYADWVPFQTKGLAPASAPQNLHAIHTDSGLILEWEEVIP

Parental  EAPLEGPLGPYKLSWVQDNGTQDELTVEGTRANLTGWDPQKDLIVRVCVSNAVGCGPWSQPLVVSSHDRA
          E.PLEGPLGPYKLSWV.DNGTQDELT.EGTRANLTGWDPQK.LIVRVCVS.AVGCGPWSQPLVVSSHD.A
Retrocopy EGPLEGPLGPYKLSWV*DNGTQDELTMEGTRANLTGWDPQKGLIVRVCVSSAVGCGPWSQPLVVSSHDHA

Parental  GQQGPPHSRTSWVPVVLGVLTALVTAAALALILLRKRRKETRFGQAFDSVMARGEPAVHFRAARSFNRER
          GQ.GPPHSRTSWVPVVLGVLTALVTAAALALILL.KR.KET.FGQ.FDSV..RGEPA.HF.AARSFN.ER
Retrocopy GQKGPPHSRTSWVPVVLGVLTALVTAAALALILLQKRPKETWFGQGFDSVISRGEPAIHFWAARSFNQER

Parental  PERIEATLDSLGISDELKEKLEDVLIPEQQFTL-GRMLGKGEFGSVREAQLKQEDGSFVKVAVKMLKADI
          P..IEATL.SLGI..ELKEKLEDVLIPEQQFTL.G...GKGEFGSVR.AQLKQEDGSFVKVA.KMLKAD.
Retrocopy PKCIEATLESLGINSELKEKLEDVLIPEQQFTL<GWI*GKGEFGSVR*AQLKQEDGSFVKVAMKMLKADL

Parental  IASSDIEEFLREAACMKEFDHPHVAKLVGVSLRSRAKG
          IASSDIEEFLR.AACMKEFDHPHVAKLVGVSL.....G
Retrocopy IASSDIEEFLRKAACMKEFDHPHVAKLVGVSL*ASGAG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.06 RPM	21.65 RPM
bodymap2_adrenal	0.33 RPM	3.83 RPM
bodymap2_brain	0.05 RPM	69.71 RPM
bodymap2_breast	0.02 RPM	48.17 RPM
bodymap2_colon	0.00 RPM	6.92 RPM
bodymap2_heart	0.07 RPM	3.45 RPM
bodymap2_kidney	0.00 RPM	35.92 RPM
bodymap2_liver	0.04 RPM	1.67 RPM
bodymap2_lung	0.00 RPM	8.93 RPM
bodymap2_lymph_node	0.02 RPM	12.30 RPM
bodymap2_ovary	0.02 RPM	125.49 RPM
bodymap2_prostate	0.00 RPM	5.30 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.04 RPM
bodymap2_testis	0.02 RPM	53.15 RPM
bodymap2_thyroid	0.02 RPM	3.46 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1598 was not detected

EST

1 EST(s) were mapped to retro_hsap_1598 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF367454	76552545	76553028	97.1	466	14	449

TSS

No TSS is located nearby retro_hsap_1598 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CTAGGCTCAAGCGATCCACCTATC (24 nt long)
• Reverse primer: CGCTGACTGGGATGAACCAGTTCT (24 nt long)
• Annealing temperature: 63 °C
• (Expected) product size: 519
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1598 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092445	1 retrocopy	retro_hsap_1598 ,
Macaca mulatta	ENSMMUG00000013803	1 retrocopy	retro_mmul_2227,