RetrogeneDB ID: retro_hsap_4319

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: GL000205.1:39066..39560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDSP2
• Ensembl ID: ENSG00000175215
• Aliases: CTDSP2, OS4, PSR2, SCP2
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:HGNC Symbol;Acc:17077]

Sequence

>retro_hsap_4319
ATGGAACAAGGCTCCATCATCACCCAGGCATGGAGGGAAGATGCCCTGGTCCTTACCAAGCAAGGCCTGGTTTCCAAAGT
CCTCTCCGAAGAGGCCTCATGTTTGCCACATCTTAAAAGTCCCCTTTCTGCTGTTCTTGCACCCAGCATGTTGGACAGTC
AAGTTCCCCCGCTGAGCAATCCACACATAAGGAGGGAGTCAACACCATTGCTATGTCGGATCAGCTCCAGCGTCTCCAAT
ATCAGTTTTATCAGATCCCAGGAACCTGCCTGCTCCCAGAGGTGACAGAGAAAAATCAAGGAAGGATCTGTATGGTCACT
GACCTGGATGAAACCCTTGTGCATAGCTCCTTTAAGCCAATCAGCAATGCTGACTGCCTAGTGCCTGTAGAGCTTGAGGG
GACCATGCACCAGATCCATGTGCTCATGAGGCCTTATATGGATGAGTTCCTGACATGAATGGAGGAAATGTTTAAATGTG
TTTTCGTCATTGCT

Alignment

ORF - retro_hsap_4319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 60.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEHGSIITQARREDALVLTKQGLVSK-SSPKKPRGRNIFK-ALFCCFRAQHVGQSSSSTELAAYKEEANT
          ME.GSIITQA.REDALVLTKQGLVSK.SSPK.P....I.K...FCC...QHVGQSSS..E....KE..NT
Retrocopy MEQGSIITQAWREDALVLTKQGLVSK>SSPKRPHVCHILK>SPFCCSCTQHVGQSSSPAEQSTHKEGVNT

Parental  IAKSDLLQCLQYQFYQIPGTCLLPEVTEEDQGRICVVIDLDETLVHSSFKPINNADFIVPIEIEGTTHQV
          IA.SD.LQ.LQYQFYQIPGTCLLPEVTE..QGRIC.V.DLDETLVHSSFKPI.NAD..VP.E.EGT.HQ.
Retrocopy IAMSDQLQRLQYQFYQIPGTCLLPEVTEKNQGRICMVTDLDETLVHSSFKPISNADCLVPVELEGTMHQI

Parental  YVLKRPYVDEFLRRMGELFECVLFTA
          .VL.RPY.DEFL..M.E.F.CV...A
Retrocopy HVLMRPYMDEFLT*MEEMFKCVFVIA

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	0.04 RPM	209.37 RPM
bodymap2_adrenal	0.12 RPM	163.69 RPM
bodymap2_brain	0.02 RPM	59.23 RPM
bodymap2_breast	0.16 RPM	177.55 RPM
bodymap2_colon	0.02 RPM	221.59 RPM
bodymap2_heart	0.00 RPM	120.61 RPM
bodymap2_kidney	0.14 RPM	140.92 RPM
bodymap2_liver	0.00 RPM	91.02 RPM
bodymap2_lung	0.00 RPM	266.49 RPM
bodymap2_lymph_node	0.00 RPM	290.83 RPM
bodymap2_ovary	0.17 RPM	211.26 RPM
bodymap2_prostate	0.00 RPM	235.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	176.11 RPM
bodymap2_testis	0.00 RPM	103.56 RPM
bodymap2_thyroid	0.00 RPM	167.05 RPM
bodymap2_white_blood_cells	0.00 RPM	473.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4319 was not detected

EST

No EST(s) were mapped for retro_hsap_4319 retrocopy.

TSS

No TSS is located nearby retro_hsap_4319 retrocopy 5' end.

Lab

retro_hsap_4319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000137770	1 retrocopy	retro_hsap_4881,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319 ,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402, retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.81 RPM
CEU_NA11843	0.34 RPM
CEU_NA11930	0.88 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.95 RPM
CEU_NA12751	1.68 RPM
CEU_NA12760	0.85 RPM
CEU_NA12827	0.42 RPM
CEU_NA12872	0.60 RPM
CEU_NA12873	1.02 RPM
FIN_HG00183	0.77 RPM
FIN_HG00277	2.33 RPM
FIN_HG00315	0.41 RPM
FIN_HG00321	1.24 RPM
FIN_HG00328	0.33 RPM
FIN_HG00338	0.40 RPM
FIN_HG00349	0.26 RPM
FIN_HG00375	0.37 RPM
FIN_HG00377	0.35 RPM
FIN_HG00378	0.55 RPM
GBR_HG00099	0.84 RPM
GBR_HG00111	0.86 RPM
GBR_HG00114	0.26 RPM
GBR_HG00119	0.93 RPM
GBR_HG00131	1.01 RPM
GBR_HG00133	0.60 RPM
GBR_HG00134	1.07 RPM
GBR_HG00137	0.38 RPM
GBR_HG00142	1.33 RPM
GBR_HG00143	0.51 RPM
TSI_NA20512	0.31 RPM
TSI_NA20513	1.26 RPM
TSI_NA20518	0.61 RPM
TSI_NA20532	0.58 RPM
TSI_NA20538	0.78 RPM
TSI_NA20756	1.19 RPM
TSI_NA20765	0.73 RPM
TSI_NA20771	0.60 RPM
TSI_NA20786	0.31 RPM
TSI_NA20798	0.81 RPM
YRI_NA18870	0.68 RPM
YRI_NA18907	0.76 RPM
YRI_NA18916	0.74 RPM
YRI_NA19093	0.57 RPM
YRI_NA19099	1.12 RPM
YRI_NA19114	0.89 RPM
YRI_NA19118	0.68 RPM
YRI_NA19213	1.03 RPM
YRI_NA19214	0.37 RPM
YRI_NA19223	1.01 RPM

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Indel association:

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