RetrogeneDB ID: retro_hsap_1360

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:69328478..69328775(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000270975
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSG00000111196
• Aliases: None
• Description: mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]

Sequence

>retro_hsap_1360
ATGGTTATGGCTAGCGATTTCTACCTGCGCTACTACGTAGGGCACAAGGGCAAGTTTGGGCATGAGTTTTTGGAGTCCGA
ATTTCAGCTGGATGGAAAGCTTAGATATGCCAACAGTAGCAATTACAAAAATGACGTCATGATCAGAAAAGAGGCTTACG
TGCACAAGAGTTTAATGGAAGAACTGAAGAGAATTATTGATGACAATGAAATCACAAAAGAAGATGATGGTTTGTGGCCT
CCCCCTGACAGGGCTGGCCGACAGGAGCTTGAAATTGTAATTGGAGATGAGCACATA

Alignment

ORF - retro_hsap_1360 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 66.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
          M..ASDFYLRYYVGHKGKFGHEFLE.EF..DGKLRYAN.SNYKNDVMIRKEAYVHKS.MEELKRIIDD.E
Retrocopy MVMASDFYLRYYVGHKGKFGHEFLESEFQLDGKLRYANSSNYKNDVMIRKEAYVHKSLMEELKRIIDDNE

Parental  ITKEDDALWPPPDRVGRQELEIVIGDEHI
          ITKEDD.LWPPPDR.GRQELEIVIGDEHI
Retrocopy ITKEDDGLWPPPDRAGRQELEIVIGDEHI

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	8.13 RPM
bodymap2_adrenal	0.14 RPM	10.91 RPM
bodymap2_brain	0.00 RPM	7.52 RPM
bodymap2_breast	0.06 RPM	11.42 RPM
bodymap2_colon	0.00 RPM	9.15 RPM
bodymap2_heart	0.00 RPM	4.45 RPM
bodymap2_kidney	0.00 RPM	10.09 RPM
bodymap2_liver	0.00 RPM	9.70 RPM
bodymap2_lung	0.00 RPM	4.75 RPM
bodymap2_lymph_node	0.00 RPM	6.96 RPM
bodymap2_ovary	0.04 RPM	16.19 RPM
bodymap2_prostate	0.02 RPM	15.19 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.95 RPM
bodymap2_testis	0.00 RPM	14.22 RPM
bodymap2_thyroid	0.00 RPM	13.54 RPM
bodymap2_white_blood_cells	0.00 RPM	8.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1360 was not detected

EST

No EST(s) were mapped for retro_hsap_1360 retrocopy.

TSS

No TSS is located nearby retro_hsap_1360 retrocopy 5' end.

Lab

retro_hsap_1360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1360 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_932

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Callithrix jacchus	ENSCJAG00000021662	7 retrocopies	retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250, retro_cjac_546,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens	ENSG00000111196	1 retrocopy	retro_hsap_1360 ,
Homo sapiens	ENSG00000162385	2 retrocopies	retro_hsap_1803, retro_hsap_3318,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Nomascus leucogenys	ENSNLEG00000003355	1 retrocopy	retro_nleu_1395,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Pan troglodytes	ENSPTRG00000004679	2 retrocopies	retro_ptro_1179, retro_ptro_932,
Ictidomys tridecemlineatus	ENSSTOG00000000835	1 retrocopy	retro_itri_212,
Tupaia belangeri	ENSTBEG00000014820	7 retrocopies	retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta	ENSTSYG00000010452	7 retrocopies	retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.05 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	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 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	0.02 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).