RetrogeneDB ID: retro_hsap_2709

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:135874391..135874810(+)
• Located in intron of: ENSG00000174579

Retrocopy information

• Ensembl ID: ENSG00000241438
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TDGF1
• Ensembl ID: ENSG00000241186
• Aliases: TDGF1, CR, CRGF, CRIPTO
• Description: teratocarcinoma-derived growth factor 1 [Source:HGNC Symbol;Acc:11701]

Sequence

>retro_hsap_2709
CCATCTCAGGGAGACCTGGCCTTCAGAGATGACAGCATTCAACCCCAAGAGGAGCCTGCTTTTCATCCTCAGCCTTCCCA
ACCTGTGCCGCCCATGGGGATACAGGACAGTAACGAGCTAAACAAAACCTGCTGCCTGAATGGGGGGAACTTGTATGCTG
GGGTCCTTTTGTGCCTGCTTCCCCTCCTTCTACAGACGGAATTGTGAGCACCATGTACGTATGCAAAGAGAACTGTGGGT
CTGTGCCCCGTGACACCCGGCTGCCCAAGAACTGTTCTATGTGTAAATGCTGGCATGGCCAGCTCCGCTGCTTTCCTCAG
GCATTTCTACCTGGCTGTGATGGCCTTGTGATGGATGAGCACCTCATGGTTTCCAATACTCCAGAACTACTACTGTCTGC
ATGTACCACTCTTATGCTT

Alignment

ORF - retro_hsap_2709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.34 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSRGYLAFRDDSIWPQEEPAIRPRSSQRVPPMGIQHSKELNRTCCLNGG-TCML-GSFC-ACPPSFYGRN
          PS.G.LAFRDDSI.PQEEPA..P..SQ.VPPMGIQ.S.ELN.TCCLNGG.TCML.G.F..A.PPS..G..
Retrocopy PSQGDLAFRDDSIQPQEEPAFHPQPSQPVPPMGIQDSNELNKTCCLNGG>TCML>GPFVPASPPSTDGIV

Parental  CEHDVRKENCGSVPHDTWLPKKCSLCKCWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPELPPSARTTTF
          ....V.KENCGSVP.DT.LPK.CS.CKCWHGQLRCFPQAFLPGCDGLVMDEHL..S.TPEL..SA.TT..
Retrocopy STMYVCKENCGSVPRDTRLPKNCSMCKCWHGQLRCFPQAFLPGCDGLVMDEHLMVSNTPELLLSACTTLM

Parental  M
          .
Retrocopy L

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	0.02 RPM	0.46 RPM
bodymap2_adrenal	0.45 RPM	0.18 RPM
bodymap2_brain	0.16 RPM	0.21 RPM
bodymap2_breast	0.08 RPM	0.39 RPM
bodymap2_colon	0.00 RPM	1.86 RPM
bodymap2_heart	0.00 RPM	0.96 RPM
bodymap2_kidney	0.31 RPM	19.73 RPM
bodymap2_liver	0.00 RPM	1.22 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.09 RPM	1.50 RPM
bodymap2_ovary	0.12 RPM	10.16 RPM
bodymap2_prostate	0.00 RPM	0.24 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.29 RPM
bodymap2_testis	0.17 RPM	3.64 RPM
bodymap2_thyroid	0.06 RPM	1.71 RPM
bodymap2_white_blood_cells	0.18 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2709 was not detected

EST

No EST(s) were mapped for retro_hsap_2709 retrocopy.

TSS

No TSS is located nearby retro_hsap_2709 retrocopy 5' end.

Lab

retro_hsap_2709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2709 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1831

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002174	3 retrocopies	retro_cjac_1594, retro_cjac_4151, retro_cjac_938,
Felis catus	ENSFCAG00000014508	1 retrocopy	retro_fcat_714,
Homo sapiens	ENSG00000241186	7 retrocopies	retro_hsap_1999, retro_hsap_2393, retro_hsap_2709 , retro_hsap_3415, retro_hsap_3956, retro_hsap_4737, retro_hsap_4804,
Gorilla gorilla	ENSGGOG00000003453	5 retrocopies	retro_ggor_1447, retro_ggor_1815, retro_ggor_2307, retro_ggor_2943, retro_ggor_2990,
Loxodonta africana	ENSLAFG00000009140	4 retrocopies	retro_lafr_1037, retro_lafr_1067, retro_lafr_757, retro_lafr_871,
Microcebus murinus	ENSMICG00000016492	1 retrocopy	retro_mmur_635,
Macaca mulatta	ENSMMUG00000003088	6 retrocopies	retro_mmul_1744, retro_mmul_2290, retro_mmul_2560, retro_mmul_742, retro_mmul_770, retro_mmul_967,
Mustela putorius furo	ENSMPUG00000015167	1 retrocopy	retro_mputfur_961,
Mus musculus	ENSMUSG00000032494	3 retrocopies	retro_mmus_1429, retro_mmus_1544, retro_mmus_1908,
Nomascus leucogenys	ENSNLEG00000006143	6 retrocopies	retro_nleu_1649, retro_nleu_2124, retro_nleu_2179, retro_nleu_2317, retro_nleu_2519, retro_nleu_535,
Otolemur garnettii	ENSOGAG00000017039	1 retrocopy	retro_ogar_2611,
Pan troglodytes	ENSPTRG00000014854	7 retrocopies	retro_ptro_1333, retro_ptro_1749, retro_ptro_1831, retro_ptro_2319, retro_ptro_2685, retro_ptro_3153, retro_ptro_3194,
Tarsius syrichta	ENSTSYG00000013609	2 retrocopies	retro_tsyr_295, retro_tsyr_574,
Tursiops truncatus	ENSTTRG00000017299	1 retrocopy	retro_ttru_441,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).