RetrogeneDB ID: retro_hsap_934

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:121232561..121233631(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BMPR1A
• Ensembl ID: ENSG00000107779
• Aliases: None
• Description: bone morphogenetic protein receptor, type IA [Source:HGNC Symbol;Acc:1076]

Sequence

>retro_hsap_934
TGGAGACATTATTGCAAGAGCATCTCAAGCAGACGTCGTTACAATCGTGATTTGGAACGGATGAAGCATTTATTCCAGTT
GGAGAATCACTAAAAGACCTTATTGACCAGTCACAAAGTTCTGGTAGTGGGTCTGGACTACCTTTATTGGTTCAGCGAAC
TATTGCCAAACAGATTCAGATGGTCCGGCAAGTTGGTAAAGGCCGATATGGAGAAGTATGGATGGGCAAATGGCGTGGCG
AAAAAGTGGCGGTGAAAGTATTCTTTACCACTGAAGAAGCCAGCTGGTTTCGAGAAACAGAAATCTACCAAACTGTGCTA
ATGCGCCATGAAAACATACTTGGTTTCATAGCAGCAGACATTAAAGGTACAGGTTCCTGGACTCAGCTCTATTTGATTAC
TGATTACCATGAAAATGGATCTCTCTATGACTTCCTGAAATGTGCTACACTGGACACCAGAGCCCTGCTTAAATCGGCTT
ATTCAGCTGCCTGTGGTCTGTGCCACCTGCACACAGAAATTTATGGCACCCAAGGAAAGCCCGCAATTGCTCATCGAGAC
CTAAAGAGCAAAAACATCCTCATCAAGAAAAATGGGAGTTGCTGCATTGCTGACCTGGGCCTTGCTGTTAAATTCAACAG
TGACACAAATGAAGTTGATGTGCCCTTGAATACCAGGGTGGGCACCAAACGCTATATGGCTCCAGAAGTGCTGGACGAAA
GCCTGAACAAAAACCACTTCCAGCCCTACATCATGGCTGACATCTACAGCTTCGGCCTAATCATTTGGGAGATGGCTCGT
CGTTGTATCACAGGAGGGATTGTGGAAGAGTACCAATTGCCATATTACAACATGGTACCGAGTGATCCGTCATACGAAGA
TATGCGTGAGGTTGTGTGTGTCAAACGTTTGCGGCCAATTGTGTCTAATCGGTGGAACAGTGATGAATGTCTACGAGCAG
TTTTGAAGCTAATGTCAGAATGCTGGGCCCACAATCCAGCCTCCAGACTCACAGCGTTGAGAATTAAGAAGATGCTTGCC
AAGATGGTTGAATCCCAAGATGTAAAAATC

Alignment

ORF - retro_hsap_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.32 %
• Parental protein coverage: 67.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YKHYCKSISSRRRYNRDLEQ-DEAFIPVGESLKDLIDQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGR
          ..HYCKSISSRRRYNRDLE..DEAFIPVGESLKDLIDQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGR
Retrocopy WRHYCKSISSRRRYNRDLER<DEAFIPVGESLKDLIDQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGR

Parental  YGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHEN
          YGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHEN
Retrocopy YGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHEN

Parental  GSLYDFLKCATLDTRALLKLAYSAACGLCHLHTEIYGTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLA
          GSLYDFLKCATLDTRALLK.AYSAACGLCHLHTEIYGTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLA
Retrocopy GSLYDFLKCATLDTRALLKSAYSAACGLCHLHTEIYGTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLA

Parental  VKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKNHFQPYIMADIYSFGLIIWEMARRCITGGIVEEYQ
          VKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKNHFQPYIMADIYSFGLIIWEMARRCITGGIVEEYQ
Retrocopy VKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKNHFQPYIMADIYSFGLIIWEMARRCITGGIVEEYQ

Parental  LPYYNMVPSDPSYEDMREVVCVKRLRPIVSNRWNSDECLRAVLKLMSECWAHNPASRLTALRIKKTLAKM
          LPYYNMVPSDPSYEDMREVVCVKRLRPIVSNRWNSDECLRAVLKLMSECWAHNPASRLTALRIKK.LAKM
Retrocopy LPYYNMVPSDPSYEDMREVVCVKRLRPIVSNRWNSDECLRAVLKLMSECWAHNPASRLTALRIKKMLAKM

Parental  VESQDVKI
          VESQDVKI
Retrocopy VESQDVKI

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	0.02 RPM	25.94 RPM
bodymap2_adrenal	0.00 RPM	23.19 RPM
bodymap2_brain	0.05 RPM	23.25 RPM
bodymap2_breast	0.00 RPM	38.81 RPM
bodymap2_colon	0.04 RPM	48.53 RPM
bodymap2_heart	0.00 RPM	21.06 RPM
bodymap2_kidney	0.00 RPM	25.77 RPM
bodymap2_liver	0.00 RPM	5.73 RPM
bodymap2_lung	0.00 RPM	27.41 RPM
bodymap2_lymph_node	0.00 RPM	12.92 RPM
bodymap2_ovary	0.04 RPM	46.86 RPM
bodymap2_prostate	0.10 RPM	54.02 RPM
bodymap2_skeletal_muscle	0.00 RPM	18.24 RPM
bodymap2_testis	0.04 RPM	38.54 RPM
bodymap2_thyroid	0.00 RPM	64.57 RPM
bodymap2_white_blood_cells	0.00 RPM	5.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_934 was not detected

EST

No EST(s) were mapped for retro_hsap_934 retrocopy.

TSS

No TSS is located nearby retro_hsap_934 retrocopy 5' end.

Lab

retro_hsap_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_934 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000107779	2 retrocopies	retro_hsap_3659, retro_hsap_934 ,
Gorilla gorilla	ENSGGOG00000003720	1 retrocopy	retro_ggor_2471,
Pan troglodytes	ENSPTRG00000002706	1 retrocopy	retro_ptro_2482,
Rattus norvegicus	ENSRNOG00000010814	1 retrocopy	retro_rnor_2707,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.36 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).