RetrogeneDB ID: retro_hsap_2811

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:88144699..88145118(-)
• Located in intron of: ENSG00000229729

Retrocopy information

• Ensembl ID: ENSG00000241535
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSG00000094916
• Aliases: CBX5, HEL25, HP1, HP1A
• Description: chromobox homolog 5 [Source:HGNC Symbol;Acc:1555]

Sequence

>retro_hsap_2811
GGAAAGAAAACCAAGCACACAGCTAACATTTCATCAGAGAATGAAGAGGAGTAGACTGTGGAGAAGGTGCTAGACAGGCA
TGTGGTTAAGTGGCAAGTGGAGTATCTGCTGAAGTGGAAAGGCTTTTCTGAGGAGCACAATACTTGGGAATCTGAGAAAA
ACTTGGATTGCCTTTAGCTCATTTCTTAGTTTACAAAAAAGTTTAAGATGATGAAGGAGGGTTAAAATAACAAGCCTGGG
GAGAAGTCAAAAAGTAGCAAAGAAATCCAATTTCTCAAACTGTGCTGACAGTATCAAGTCCAAAAAAGAGAACAGAGTGA
TGATATTGCTTGGGGCTTCGAGATAAGACTAGAACCAGAAAAGATCATTGGGGCAACAGATTCCTGTGGCAATTTATGTT
TTTAATGAAATGGAAAGAC

Alignment

ORF - retro_hsap_2811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKYK
          GKKTK.TA..SS.E.EEE..VEKVLDR.VVK.QVEYLLKWKGFSEEHNTWE.EKNLDC..LIS.F.KK.K
Retrocopy GKKTKHTANISS-ENEEE*TVEKVLDRHVVKWQVEYLLKWKGFSEEHNTWESEKNLDCL*LIS*FTKKFK

Parental  KMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDL-MFLM
          .MKEG.NNKP.EKS.S.K....F..........K.......IA.GFE..LEPEKIIGATDSCG.L.MFLM
Retrocopy MMKEG*NNKPGEKSKSSK-EIQFLKLC*QYQVQKREQSDD-IAWGFEIRLEPEKIIGATDSCGNL<MFLM

Parental  KWKD
          KWKD
Retrocopy KWKD

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	108.37 RPM
bodymap2_adrenal	0.14 RPM	130.00 RPM
bodymap2_brain	0.23 RPM	239.16 RPM
bodymap2_breast	0.00 RPM	126.07 RPM
bodymap2_colon	0.00 RPM	96.49 RPM
bodymap2_heart	0.02 RPM	95.20 RPM
bodymap2_kidney	0.00 RPM	178.84 RPM
bodymap2_liver	0.00 RPM	38.40 RPM
bodymap2_lung	0.00 RPM	77.81 RPM
bodymap2_lymph_node	0.00 RPM	130.20 RPM
bodymap2_ovary	0.00 RPM	382.55 RPM
bodymap2_prostate	0.00 RPM	78.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	34.98 RPM
bodymap2_testis	0.00 RPM	170.26 RPM
bodymap2_thyroid	0.00 RPM	164.55 RPM
bodymap2_white_blood_cells	0.00 RPM	99.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2811 was not detected

EST

No EST(s) were mapped for retro_hsap_2811 retrocopy.

TSS

No TSS is located nearby retro_hsap_2811 retrocopy 5' end.

Lab

retro_hsap_2811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2811 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1905
Gorilla gorilla	retro_ggor_1955
Pongo abelii	retro_pabe_2307

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811 ,
Homo sapiens	ENSG00000108468	3 retrocopies	retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Homo sapiens	ENSG00000122565	9 retrocopies	retro_hsap_1071, retro_hsap_1145, retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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