RetrogeneDB ID: retro_hsap_2649

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:52407411..52408910(+)
• Located in intron of: ENSG00000114841

Retrocopy information

• Ensembl ID: ENSG00000239557
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP2R5C
• Ensembl ID: ENSG00000078304
• Aliases: PPP2R5C, B56G, PR61G
• Description: protein phosphatase 2, regulatory subunit B', gamma [Source:HGNC Symbol;Acc:9311]

Sequence

>retro_hsap_2649
ATGCCGAATAAAACAAGAAGGAGAAAGAATCACCAAAAGCAGGGAAGAGTGGAAAAAGTTCAAAAGAAGGACAAGACACA
GTAGAATCAGAGCAAATTTCCGTCAGGAAAAACAGCCTTGTTGCTGTCCCGTCTACAGTGTCTGCTAAAATAAAAGTACC
CGTCTCTCAGCCCATAGTGAAGAAAGACAAACAGCAAAATTCTTCAAGGTTTAGCGCAAGCAGTAATAGAGAACTTCAAA
AACTACCATCCTTAAAAGATGTTCCTCCTGCTGATCAAAAGAAGTTTTTTATCCAGAAGTTATGTCAGTGTTGCGTCCTT
TTTGACTTTGTTTCTGATCCACTAAGTGAACTAAAGTAGAAGGAATTAAAACGAGCTGCTTTAAGTGAAATGGTAGAATA
TATCACCCATAATTGGAATGTGATCACAGAGCCTGTTTACCCAGAAGTAGTCCATATGTTTGCAGTTAACATGTTTCGAA
TATTACCACCTTCCTCCAATCCTACGGGAGCAGAATTTGACTCAGAGGAAGATGAACCAACGTTAGAAGCAGGCTGGCTT
CATCTACACTTATTTATGAATTTTTCTTAAGATTTTTAGAGTCTGCAGATTTCCAATCTAATATAGCGAAGAAATATATT
GATCAGAAGTTTGTATTGCAGCTTTTAAAGCTCTTTGACAGTGAAGATCCTCAGGAGAGAGATTTTCTTAAAACCACCCT
TCACAGAATCTATGGGAAATTCCTAGGCTTGAGAGCTTACATCAGAAAACAGATAAATAATATATTTTATAGGTTTATTT
ATGAAACAGAGCATCATAATGGCATAGCAGAGTTACTGGAAATATTGGGAAGTATAATTAATGGATTTGCCTTACCACTA
AAAGAAGAACACAAGATTTTCTTATTGAAGGTGTTACTACCTTTGCACAAAGTGAAATCTCTTGAGTGTCTACCACCCCC
AGCTGGCATACTGTGGAGTGCAGTTTTTAGAAAAGGACAGCACCCCCACAGAACCAGTGGTGATGACACTTCTCAAATGC
TGGCCAAAGACTCACAGTCCAAAAGAAGTAATGTTCTTAAACAAATTAGAAGCGATTTTAGATGTCATTGAACCATCAGA
ATTTGTGAAGACCATGGAGCCCCTCTTCCGGCAGTTGGCCAAATGTGTCTCCAGCCCACACTTCCAGGTGGCAGAGCGAG
CTCTCTATTACTGGAATAATGAATACATCATGAGTTTAATCAGTGACAATGCAGCGAAGATTCTGCCCATCATGTTTCCT
TCCTTGTACCACAACTCAAAGACCCATTGGAACAAGATAATACATGGCTTGATATACAACGCCCTGAATCTGTTCATAGA
GATGGAACAAAAGCTGTTTGATGACTGTACACAACAGTCCAAAGCAGAGAAACTAAAAGAGAAGCTAAAAATGGAAGTAC
GAGAAGAAGCATGGGTTAAAATAGAAAATCTAGCCAAAGCCAATCCCCAGGTACTAAAA

Alignment

ORF - retro_hsap_2649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 92.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPNK-NKKEKESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQPIVKKDKRQNSS
          MPNK.NKKEKESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQPIVKKDK.QNSS
Retrocopy MPNK<NKKEKESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQPIVKKDKQQNSS

Parental  RFSASNNRELQKLPSLKDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNR
          RFSAS.NRELQKLPSLKDVPPADQ.K.FIQKL.QCCVLFDFVSDPLS.LK.KE.KRAALSEMVEYITHN.
Retrocopy RFSASSNRELQKLPSLKDVPPADQKKFFIQKLCQCCVLFDFVSDPLSELK*KELKRAALSEMVEYITHNW

Parental  NVITEPIYPEVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRFLESPDFQPN
          NVITEP.YPEVVHMFAVNMFR.LPPSSNPTGAEFD.EEDEPTLEA.W.HL.L..YEFFLRFLES.DFQ.N
Retrocopy NVITEPVYPEVVHMFAVNMFRILPPSSNPTGAEFDSEEDEPTLEAGWLHLHL<IYEFFLRFLESADFQSN

Parental  IAKKYIDQKFVLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAE
          IAKKYIDQKFVLQLL.LFDSEDP.ERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAE
Retrocopy IAKKYIDQKFVLQLLKLFDSEDPQERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAE

Parental  LLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSL-SVYHPQLAYCVVQFLEKDSTLTEPVVMALLKY
          LLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSL.SVYHPQLAYC.VQFLEKDST.TEPVVM.LLK.
Retrocopy LLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSL>SVYHPQLAYCGVQFLEKDSTPTEPVVMTLLKC

Parental  WPKTHSPKEVMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDN
          WPKTHSPKEVMFLN.LE.ILDVIEPSEFVK.MEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDN
Retrocopy WPKTHSPKEVMFLNKLEAILDVIEPSEFVKTMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDN

Parental  AAKILPIMFPSLYRNSKTHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKEREEAWVK
          AAKILPIMFPSLY.NSKTHWNK.IHGLIYNAL.LF.EM.QKLFDDCTQQ.KAEKLKEKLKM..REEAWVK
Retrocopy AAKILPIMFPSLYHNSKTHWNKIIHGLIYNALNLFIEMEQKLFDDCTQQSKAEKLKEKLKMEVREEAWVK

Parental  IENLAKANPQAQK
          IENLAKANPQ..K
Retrocopy IENLAKANPQVLK

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	146.50 RPM
bodymap2_adrenal	0.92 RPM	164.45 RPM
bodymap2_brain	0.19 RPM	151.94 RPM
bodymap2_breast	0.31 RPM	131.34 RPM
bodymap2_colon	0.02 RPM	166.29 RPM
bodymap2_heart	0.00 RPM	171.91 RPM
bodymap2_kidney	0.02 RPM	97.76 RPM
bodymap2_liver	0.00 RPM	46.56 RPM
bodymap2_lung	0.70 RPM	140.68 RPM
bodymap2_lymph_node	0.29 RPM	166.98 RPM
bodymap2_ovary	0.00 RPM	131.70 RPM
bodymap2_prostate	0.00 RPM	164.18 RPM
bodymap2_skeletal_muscle	0.02 RPM	72.11 RPM
bodymap2_testis	0.08 RPM	170.21 RPM
bodymap2_thyroid	0.13 RPM	150.46 RPM
bodymap2_white_blood_cells	0.04 RPM	335.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2649 was not detected

EST

No EST(s) were mapped for retro_hsap_2649 retrocopy.

TSS

No TSS is located nearby retro_hsap_2649 retrocopy 5' end.

Lab

retro_hsap_2649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2649 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1784
Gorilla gorilla	retro_ggor_1850
Pongo abelii	retro_pabe_2322

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000078304	2 retrocopies	retro_hsap_2649 , retro_hsap_3796,
Nomascus leucogenys	ENSNLEG00000015727	2 retrocopies	retro_nleu_1125, retro_nleu_655,
Otolemur garnettii	ENSOGAG00000006274	1 retrocopy	retro_ogar_1944,
Pongo abelii	ENSPPYG00000006152	3 retrocopies	retro_pabe_2322, retro_pabe_2414, retro_pabe_3101,
Pan troglodytes	ENSPTRG00000006734	1 retrocopy	retro_ptro_1784,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.29 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.33 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.33 RPM
FIN_HG00328	0.40 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.19 RPM
GBR_HG00114	0.34 RPM
GBR_HG00119	0.26 RPM
GBR_HG00131	0.37 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.22 RPM
GBR_HG00137	0.30 RPM
GBR_HG00142	0.33 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.41 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.17 RPM
TSI_NA20765	0.25 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.21 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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