RetrogeneDB ID: retro_hsap_3734

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:57484523..57485383(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235368
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAPCD2
• Ensembl ID: ENSG00000186193
• Aliases: SAPCD2, C9orf140, p42.3
• Description: suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]

Sequence

>retro_hsap_3734
CCACGCCCCAGCCCGGCCCGGCCCGGGAACCAGCCGACGCAGCGCCTGCTGTTCGCGCCGGCCGACGAGCCGCGGATGGT
CCCGGAGAGGAAGCCCCTGCCCCTGGGCGAGCGCGCTTCTCTGGCTTGTCCCAGCCGCGCGGCCCGCAGCCCAGAGCAGC
TGTGCGCCCCCGCCGAGGCGGCGCCCTGCCCCGTGGAACCGGAGCGGTCCCAGAGCGCGGTCCTGGAACAGAGCCCCAGC
GCGGACGCAGGTGCAGCGACCTGCAGGGCCTTGGAGGCAGACTCAGGGGATGCCCCGCGGGGCCCAGCGCCCGAGGAGAA
CGTCAGAGGCACACCATCACCAGCGGCGTGGACTGCGGCCTGCTGAAGCAGATGAAGGAGCTGGAGCAGGAGAAGGAGGT
GCTGCTGCAGGGTTTGGAGATGATGGCGCGGGGCCGTGATTGGTACCAGCAGCAGCTGCAACGGGTGCAGGAGCGCCAGT
GCCGCCTGGGCCAGAGCAGAGCCAGCGCCGACTTTGGGGCCACGGGGAGCCCCCGCCCACTGGGGCGGCTACTGTCCAAG
GTACAGGAGGTGACCAGGTGCCTGGGGGAGCTGCTGGCTGCGGCCTGTGCCAGCTGGGCCCTGCCCACGTCCTCCGCCGG
GCCCCCTGCTCTGCCCTAAGGTCAACCTCGTCCCCGGGCTGTCAGCAGCAGACCATCCTCATGCTGAAGGAGCAGAACTG
ACTCCTTACCCAGGAGGCGACCGAGAAGAGTGAGTGCATCACGCAGCTGGAGCAAGAGAAGTCAGCGCTCATTAAGCAGC
TGTTTGAGGCCCGCGCCCTGAGCCAGCAGGACGGGGGGGCCTCTGGACCCCACCTTCATC

Alignment

ORF - retro_hsap_3734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 73.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTRAPARPGDQPPPPPQRLVFAPADEPRTVLERKPLPLGVRAPLAGPSAAARSPEQLCAPAEAAPCPAEP
          P...PARPG.Q...P.QRL.FAPADEPR.V.ERKPLPLG.RA.LA.PS.AARSPEQLCAPAEAAPCP.EP
Retrocopy PRPSPARPGNQ---PTQRLLFAPADEPRMVPERKPLPLGERASLACPSRAARSPEQLCAPAEAAPCPVEP

Parental  ERSQSAALEPSSSADAGAVACRALEADSGDARRAPR-ARGERRRHTIASGVDCGLLKQMKELEQEKEVLL
          ERSQSA.LE.S.SADAGA..CRALEADSGDA.R.P..ARGER.RHTI.SGVDCG................
Retrocopy ERSQSAVLEQSPSADAGAATCRALEADSGDAPRGPA<ARGERQRHTITSGVDCGXXXXXXXXXXXXXXXX

Parental  QGLEMMARGRDWYQQQLQRVQERQRRLGQSRASADFGAAGSPRPLGRLLPKVQEVARCLGELLAAACASR
          ..LEMMARGRDWYQQQLQRVQERQ.RLGQSRASADFGA.GSPRPLGRLL.KVQEV.RCLGELLAAACAS.
Retrocopy XXLEMMARGRDWYQQQLQRVQERQCRLGQSRASADFGATGSPRPLGRLLSKVQEVTRCLGELLAAACASW

Parental  ALPPSSSGP-PCPALTSTSPPVWQQQTILMLKEQNRLLTQEVTEKSERITQLEQEKSALIKQLFEARALS
          ALP.SS.GP.PC.AL.STS.P..QQQTILMLKEQN.LLTQE.TEKSE.ITQLEQEKSALIKQLFEARALS
Retrocopy ALPTSSAGP<PCSALRSTSSPGCQQQTILMLKEQN*LLTQEATEKSECITQLEQEKSALIKQLFEARALS

Parental  QQD-GGPLDSTFI
          QQD.GGPLD.TFI
Retrocopy QQD>GGPLDPTFI

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	0.00 RPM	0.06 RPM
bodymap2_adrenal	0.00 RPM	0.74 RPM
bodymap2_brain	0.00 RPM	4.73 RPM
bodymap2_breast	0.00 RPM	0.76 RPM
bodymap2_colon	0.00 RPM	1.84 RPM
bodymap2_heart	0.00 RPM	0.15 RPM
bodymap2_kidney	0.00 RPM	0.81 RPM
bodymap2_liver	0.00 RPM	0.02 RPM
bodymap2_lung	0.00 RPM	0.35 RPM
bodymap2_lymph_node	0.00 RPM	2.49 RPM
bodymap2_ovary	0.00 RPM	0.10 RPM
bodymap2_prostate	0.00 RPM	1.63 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.00 RPM	0.36 RPM
bodymap2_thyroid	0.00 RPM	0.49 RPM
bodymap2_white_blood_cells	0.00 RPM	1.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3734 was not detected

EST

No EST(s) were mapped for retro_hsap_3734 retrocopy.

TSS

No TSS is located nearby retro_hsap_3734 retrocopy 5' end.

Lab

retro_hsap_3734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3734 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2530

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734 , retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867, retro_nleu_2939,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222, retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530, retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,

Population studies

Expression level across human populations :

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

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Indel association:

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