RetrogeneDB ID: retro_hsap_4695

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:68004054..68004909(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213740
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSG00000142864
• Aliases: SERBP1, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_hsap_4695
AAAGAAGGAATAAGATGAATTGGAAGAACACCTGATCAACAACTTCAGGGTGGAGGGAAAATAATTGATAGAAGACCAGA
AAGGCGACCACCTTGTGAACGAAGATTTGAAAAGTCACTTGAAGAAAAGGGTGAACGAGGCGAATTTTCAGCTGATAGAC
CGATTATTGACCGACATATTCGAGGTCGTGGTAGTCTTGGAAGAGGTCGAGGGGGCCGTGGACATGGAATGGGCAGAGGA
GATGGATTTGATTCTCGTGGCAAACGTGAATTTGATAGGCATAGTGGAAGTGATAGATCTGGCCTGAAGCACGAGGACAA
ACGTGGAGGTAGCGGATCTCACAACTGGGGAACTGTTAAAGACGAATTAACTGACTTGGATCAATCAAATGTGACTGAGG
AAACACCTGAAGGTGAAGAACATCATCCAGTGGCAGCCACTGAAAATAAGGAGAATGAAGTTGAAGAGGTAAAAGAGGAG
GGTCCAAAAGAGATGACTTTGGATGAGTGGAAGGCTATTCAAAATAAGGACTGGGCAAAAGTAGAATTTAATATCCGAAA
ACCAAATGAAGGTGCTGATGGGCAGTGGAAGAAGGGATTTGTTCTTCATAAATCAAAGAGTGAAGAGGCTCATGCTGAAG
ATTCGGTTATGGACCGTCATTTCCGGAAGCCAGCAAATGATATAACGTCTCAGCTGGAGATCAATTTTGGAGACCTTGGC
CGCCCAGGACCTGGCGGCAGGGGAGGAGGAGGTGGATGTGGGCGTGGTGGGCGCCCAAACCGTGGCAGCAGGACCGGCAA
GTCAAGTGCTTCTGCTCCTGATGTGGATAACCCAGAGGCATTCCCAGCTGTGGCT

Alignment

ORF - retro_hsap_4695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEKPLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGR
          KEGIR..GR.PDQQLQG.GKIIDRRPERRPP.ERRFEK.LEEKGE.GEFS.DRPIIDR.IRGRG.LGRGR
Retrocopy KEGIR*IGRTPDQQLQGGGKIIDRRPERRPPCERRFEKSLEEKGERGEFSADRPIIDRHIRGRGSLGRGR

Parental  GGRGRGMGRGDGFDSRGKREFDRHSGSDRSGLKHEDKRGGSGSHNWGTVKDELTDLDQSNVTEETPEGEE
          GGRG.GMGRGDGFDSRGKREFDRHSGSDRSGLKHEDKRGGSGSHNWGTVKDELTDLDQSNVTEETPEGEE
Retrocopy GGRGHGMGRGDGFDSRGKREFDRHSGSDRSGLKHEDKRGGSGSHNWGTVKDELTDLDQSNVTEETPEGEE

Parental  HHPVADTENKENEVEEVKEEGPKEMTLDEWKAIQNKDRAKVEFNIRKPNEGADGQWKKGFVLHKSKSEEA
          HHPVA.TENKENEVEEVKEEGPKEMTLDEWKAIQNKD.AKVEFNIRKPNEGADGQWKKGFVLHKSKSEEA
Retrocopy HHPVAATENKENEVEEVKEEGPKEMTLDEWKAIQNKDWAKVEFNIRKPNEGADGQWKKGFVLHKSKSEEA

Parental  HAEDSVMDHHFRKPANDITSQLEINFGDLGRPGRGGRGGRGGRGRGGRPNRGSRTDKSSASAPDVDDPEA
          HAEDSVMD.HFRKPANDITSQLEINFGDLGRPG.GGRGG.GG.GRGGRPNRGSRT.KSSASAPDVD.PEA
Retrocopy HAEDSVMDRHFRKPANDITSQLEINFGDLGRPGPGGRGGGGGCGRGGRPNRGSRTGKSSASAPDVDNPEA

Parental  FPALA
          FPA.A
Retrocopy FPAVA

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	0.18 RPM	280.28 RPM
bodymap2_adrenal	0.23 RPM	259.94 RPM
bodymap2_brain	0.07 RPM	141.41 RPM
bodymap2_breast	0.14 RPM	247.26 RPM
bodymap2_colon	0.06 RPM	385.44 RPM
bodymap2_heart	0.00 RPM	165.85 RPM
bodymap2_kidney	0.35 RPM	267.30 RPM
bodymap2_liver	0.04 RPM	169.01 RPM
bodymap2_lung	0.04 RPM	255.54 RPM
bodymap2_lymph_node	0.11 RPM	246.53 RPM
bodymap2_ovary	0.10 RPM	322.71 RPM
bodymap2_prostate	0.05 RPM	279.30 RPM
bodymap2_skeletal_muscle	0.04 RPM	342.10 RPM
bodymap2_testis	0.28 RPM	334.21 RPM
bodymap2_thyroid	0.19 RPM	388.79 RPM
bodymap2_white_blood_cells	0.04 RPM	312.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4695 was not detected

EST

No EST(s) were mapped for retro_hsap_4695 retrocopy.

TSS

No TSS is located nearby retro_hsap_4695 retrocopy 5' end.

Lab

retro_hsap_4695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018538	1 retrocopy	retro_cfam_546,
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Homo sapiens	ENSG00000142864	3 retrocopies	retro_hsap_3056, retro_hsap_413, retro_hsap_4695 ,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Otolemur garnettii	ENSOGAG00000025884	1 retrocopy	retro_ogar_185,
Pan troglodytes	ENSPTRG00000023560	2 retrocopies	retro_ptro_1985, retro_ptro_317,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.28 RPM
CEU_NA11930	0.65 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.56 RPM
CEU_NA12751	0.22 RPM
CEU_NA12760	0.81 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	0.49 RPM
CEU_NA12873	0.38 RPM
FIN_HG00183	0.38 RPM
FIN_HG00277	0.67 RPM
FIN_HG00315	0.33 RPM
FIN_HG00321	0.39 RPM
FIN_HG00328	0.40 RPM
FIN_HG00338	0.23 RPM
FIN_HG00349	0.80 RPM
FIN_HG00375	0.34 RPM
FIN_HG00377	0.40 RPM
FIN_HG00378	0.30 RPM
GBR_HG00099	0.41 RPM
GBR_HG00111	0.37 RPM
GBR_HG00114	0.32 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.32 RPM
GBR_HG00133	0.31 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.41 RPM
GBR_HG00142	0.47 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.45 RPM
TSI_NA20513	0.27 RPM
TSI_NA20518	0.78 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.47 RPM
TSI_NA20765	0.46 RPM
TSI_NA20771	0.60 RPM
TSI_NA20786	0.42 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.44 RPM
YRI_NA18907	0.42 RPM
YRI_NA18916	0.23 RPM
YRI_NA19093	0.31 RPM
YRI_NA19099	0.45 RPM
YRI_NA19114	0.37 RPM
YRI_NA19118	0.29 RPM
YRI_NA19213	0.33 RPM
YRI_NA19214	0.25 RPM
YRI_NA19223	0.26 RPM

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Indel association:

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