RetrogeneDB ID: retro_hsap_4240

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:32566225..32566976(-)
• Located in intron of: ENSG00000165264

Retrocopy information

• Ensembl ID: ENSG00000232303
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DFFB
• Ensembl ID: ENSG00000169598
• Aliases: DFFB, CAD, CPAN, DFF-40, DFF2, DFF40
• Description: DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase) [Source:HGNC Symbol;Acc:2773]

Sequence

>retro_hsap_4240
AGCGTCCTCGACGATGCCGAGCTGGTGCTGCTCACCTCACGCCAGGCCTGGCAGGGCTATGTGAGTGACATCGGGTGCTT
CCTCAGTGCTTTTCGCCAGCCGCACGCGTGGCTCATCCAGGCCGCCCGGCAGCTACTGTGTGATGAGCAGGCCCCCACAG
AGGCAGAGACTGCTGGCCGACCTCCTGTACAACGTCAGCCAGAACGTCGCAGCCGACACCCGGGCTGAGGACCCGCTGTG
GTTTGAAGGCTTGGAGTCCCGATTTTGGAATAAGTCTGGCTATCTGAGATACAGCTGTGAAAGCCGGATCCGGAGTTACC
TGAGAGAGGTGAGCTCCTGCTCCTCCATGGTGGGTGCAGAGGCTCAGGAGGAATTCCTGCGGGTCCTCCGCTCCATGTGC
CAGAAGCTCCAGTCTGTGCAGTACGACGGCAGCTATACAACAGAGGAGCCAAGGGTGGCAGCCGTCTCTGCACACCGGAA
GGCTAGTTCTCCTGCCAGGGTCCCTTCGACATGGACGGCTGCTTGTCAAGATACTCCATCAACCCCTACAGTAACAGGGA
GAGCAGGCTCCTCTTCTGGACCTGGAACCTGGATCACATAGTGGAAACAAAAACGCACCATCATTCCTACACTGGTGGAA
GCAGTTAAAGAACAAGATGGAAGAGAAGTGGACTGGGAATATTTTTATGGCCTGCTTTCTACCTCAGAGAACCTAAAATT
AGTGTTGTCTGCCATAAGAAAACCACCCACA

Alignment

ORF - retro_hsap_4240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 73.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVPDNAELVLLTLGQAWQGYVSDIRRFLSAFHEPQVGLIQAAQQLLCDEQAP-QRQRLLADLLHNVSQNI
          SV.D.AELVLLT..QAWQGYVSDI..FLSAF..P...LIQAA.QLLCDEQAP.QRQRLLADLL.NVSQN.
Retrocopy SVLDDAELVLLTSRQAWQGYVSDIGCFLSAFRQPHAWLIQAARQLLCDEQAP>QRQRLLADLLYNVSQNV

Parental  AAETRAEDPPWFEGLESRFQSKSGYLRYSCESRIRSYLREVSSYPSTVGAEAQEEFLRVLGSMCQRLRSM
          AA.TRAEDP.WFEGLESRF..KSGYLRYSCESRIRSYLREVSS..S.VGAEAQEEFLRVL.SMCQ.L.S.
Retrocopy AADTRAEDPLWFEGLESRFWNKSGYLRYSCESRIRSYLREVSSCSSMVGAEAQEEFLRVLRSMCQKLQSV

Parental  QYNGSY-FDRGAKGGSRLCTPEGWFSCQGPFDMDSCLSRHSINPYSNRESRILFSTWNLDHIIE-KKRTI
          QY.GSY...RGAKGGSRLCTPEG.FSCQGPFDMD.CLSR.SINPYSNRESR.LF.TWNLDHI.E..KRTI
Retrocopy QYDGSY<YNRGAKGGSRLCTPEG*FSCQGPFDMDGCLSRYSINPYSNRESRLLFWTWNLDHIVE>QKRTI

Parental  IPTLVEAIKEQDGREVDWEYFYGLLFTSENLKLVHIVCHKKTT
          IPTLVEA.KEQDGREVDWEYFYGLL.TSENLKLV.....K..T
Retrocopy IPTLVEAVKEQDGREVDWEYFYGLLSTSENLKLVLSAIRKPPT

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	2.03 RPM
bodymap2_adrenal	0.70 RPM	5.49 RPM
bodymap2_brain	0.28 RPM	3.52 RPM
bodymap2_breast	0.33 RPM	3.37 RPM
bodymap2_colon	0.39 RPM	1.33 RPM
bodymap2_heart	0.20 RPM	1.57 RPM
bodymap2_kidney	0.50 RPM	2.13 RPM
bodymap2_liver	0.09 RPM	1.12 RPM
bodymap2_lung	0.00 RPM	1.35 RPM
bodymap2_lymph_node	0.64 RPM	12.65 RPM
bodymap2_ovary	0.54 RPM	6.09 RPM
bodymap2_prostate	0.17 RPM	5.96 RPM
bodymap2_skeletal_muscle	0.02 RPM	0.33 RPM
bodymap2_testis	0.26 RPM	2.04 RPM
bodymap2_thyroid	0.30 RPM	2.11 RPM
bodymap2_white_blood_cells	0.37 RPM	7.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4240 was not detected

EST

No EST(s) were mapped for retro_hsap_4240 retrocopy.

TSS

No TSS is located nearby retro_hsap_4240 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CAGAGGCGTTGAGTACATCT (20 nt long)
• Reverse primer: TCCTCTTCAACCTTGTCTGGG (21 nt long)
• Anneling temperature: 60 °C
• (Expected) product size: 976
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4240 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2841
Callithrix jacchus	retro_cjac_616

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002834	1 retrocopy	retro_cjac_616,
Homo sapiens	ENSG00000169598	1 retrocopy	retro_hsap_4240 ,
Gorilla gorilla	ENSGGOG00000013452	1 retrocopy	retro_ggor_2841,
Macaca mulatta	ENSMMUG00000015174	1 retrocopy	retro_mmul_1150,
Ornithorhynchus anatinus	ENSOANG00000013652	5 retrocopies	retro_oana_116, retro_oana_117, retro_oana_125, retro_oana_27, retro_oana_91,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.53 RPM
CEU_NA11843	0.45 RPM
CEU_NA11930	0.49 RPM
CEU_NA12004	0.42 RPM
CEU_NA12400	0.25 RPM
CEU_NA12751	0.78 RPM
CEU_NA12760	0.67 RPM
CEU_NA12827	0.47 RPM
CEU_NA12872	0.49 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.36 RPM
FIN_HG00277	0.63 RPM
FIN_HG00315	0.72 RPM
FIN_HG00321	0.57 RPM
FIN_HG00328	0.66 RPM
FIN_HG00338	0.47 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.81 RPM
FIN_HG00377	0.53 RPM
FIN_HG00378	0.70 RPM
GBR_HG00099	0.49 RPM
GBR_HG00111	0.62 RPM
GBR_HG00114	0.39 RPM
GBR_HG00119	0.50 RPM
GBR_HG00131	0.52 RPM
GBR_HG00133	0.72 RPM
GBR_HG00134	0.87 RPM
GBR_HG00137	0.41 RPM
GBR_HG00142	0.42 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.45 RPM
TSI_NA20513	0.87 RPM
TSI_NA20518	0.47 RPM
TSI_NA20532	0.54 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.35 RPM
TSI_NA20765	0.70 RPM
TSI_NA20771	0.34 RPM
TSI_NA20786	0.37 RPM
TSI_NA20798	0.78 RPM
YRI_NA18870	0.85 RPM
YRI_NA18907	0.42 RPM
YRI_NA18916	0.76 RPM
YRI_NA19093	0.94 RPM
YRI_NA19099	0.40 RPM
YRI_NA19114	0.81 RPM
YRI_NA19118	0.50 RPM
YRI_NA19213	0.60 RPM
YRI_NA19214	0.93 RPM
YRI_NA19223	1.13 RPM

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Indel association:

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