RetrogeneDB ID: retro_hsap_2323

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:136956686..136958073(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227347
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSG00000165119
• Aliases: HNRNPK, CSBP, HNRPK, TUNP
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_hsap_2323
ATGGAAACTGAACAGCCAGAAGAAACCTTCCCTAACACTGAAACCAGTGGTGAATTTGGTAAACGCCCTGCAGAAGATAT
GGAAGAGGAACAAGCATTTAAAAGATCTAGAAACACTGATGAGATGGTTGAATTACCCATTCTGCTTCAGAGCAAGAATG
CTGGAGCAGTGACTGGAAAAGGAGGCAAGAATATTAAGGCTCTCCATACAGACTACAACGCCAGCATTTCAGTTCTAGAC
AGCAGTGGCCCCCAGCATATATTGCATATCAGTGCTGATATCGAAACAATTGGAGAAATTCTGAAGAAAATCATCACTAC
CTTGGAAGAGGGCCCGCAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTGTGGAATACTTAA
ATTACCAACAATATAAAGGAAGGGACTTTGACTGCGAGTTGAGGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATTATT
GGGGTCAAAGGTGCTAAAATCAAAGAACTGAGAAAACACACAAACAACCATCACGCTTTTCCAGGAATGTTGTCCTCATT
TCACTGATAGAGTTGTTCTTATTGGAGGAAAACCCAATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATTTCT
GAGTCTCCCATCAAAGGACATGCACAGCCTTATGATCCCAATTTTTACGATGAAACCTATGATTATGGTGGTTTTACAAT
GGTGTTTGCTGACGACCGTGGACGCCCAGTGAGATTTCTGATGCAGGGAAGAGGTGGTTTTGACAAAATGTCTCCTGGTC
GGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGTTTATATGAGCCCTCGTCGAGGACCACCTCCCCCTCCTCCC
GGATGAGGTGGCCAGAGTGGTAGCAGAGCTCGGAATGTTCCTCTTCCTCCACCAACCACCACCTAGGGGGGAGACCTCAT
GACCTATAACAGAAAAGGGAGACCTGGAAACCGTTACGACGGCGTGGTTGATTTCAGTGCTGATGAAACTTGGGGCTCTG
CAATAGATACATGGAACGCATCAGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCCAGATATGATTATTCCTATGCA
GGGTGTCATGGCTCATATGGTGATCTTGGTGGACCTATTATTACTACACAAGTAACTATTCCCAGAGATTTGGCTGGATC
TATTATTGGCAAAGGTGGTCAGTGGACTAAACAAATCTGTCATGAGTAGGGAGCTTTGATCAAAATTGATGAGCCTTTAG
AAGGATCCGAAGATCGGATCATTACCATTACAGGAACACAGGACCAGATACAGAATGCACAGTATTTGCCGCAGAATAGT
GTGAAGCAGTATTCTGGAAAGTTTTTC

Alignment

ORF - retro_hsap_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
          METEQPEETFPNTET.GEFGKRPAEDMEEEQAFKRSRNTDEMVEL.ILLQSKNAGAV.GKGGKNIKAL.T
Retrocopy METEQPEETFPNTETSGEFGKRPAEDMEEEQAFKRSRNTDEMVELPILLQSKNAGAVTGKGGKNIKALHT

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYNAS.SV.DSSGP..IL.ISADIETIGEILKKII.TLEEG.QLPSPTATSQLPLESDAVE.LNYQ.YKG
Retrocopy DYNASISVLDSSGPQHILHISADIETIGEILKKIITTLEEGPQLPSPTATSQLPLESDAVEYLNYQQYKG

Parental  SDFDCELRLLIHQSLAGGII-GVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKII
          .DFDCELRLLIHQSLAGGII.G.K..K.K...ENTQTTI.LFQECCPH.TDRVVLIGGKP.RVVECIKII
Retrocopy RDFDCELRLLIHQSLAGGII>GSKVLKSKN*-ENTQTTITLFQECCPHFTDRVVLIGGKPNRVVECIKII

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          LDLISESPIKG.AQPYDPNFYDETYDYGGFTM.F.D.RGRPV.F.M.GRGGFD.M.PGRGGRPMPPSRRD
Retrocopy LDLISESPIKGHAQPYDPNFYDETYDYGGFTMVFADDRGRPVRFLMQGRGGFDKMSPGRGGRPMPPSRRD

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPP-PPPRG-GDLMAYDRRGRPGDRYDGMVGFSADETWDS
          Y..MSPRRGPPPPPPG.GG..GSRARN.PLPPP.PPPRG.GDLM.Y.R.GRPG.RYDG.V.FSADETW.S
Retrocopy YVYMSPRRGPPPPPPG*GGQSGSRARNVPLPPP>PPPRG<GDLMTYNRKGRPGNRYDGVVDFSADETWGS

Parental  AIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHES
          AIDTW..SEWQMAYEPQGGS.YDYSYAG..GSYGDLGGPIITTQVTIP.DLAGSIIGKGGQ..KQI.HE.
Retrocopy AIDTWNASEWQMAYEPQGGSRYDYSYAGCHGSYGDLGGPIITTQVTIPRDLAGSIIGKGGQWTKQICHE*

Parental  GASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSGKFF
          GA.IKIDEPLEGSEDRIITITGTQDQIQNAQYL.QNSVKQYSGKFF
Retrocopy GALIKIDEPLEGSEDRIITITGTQDQIQNAQYLPQNSVKQYSGKFF

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	0.10 RPM	632.24 RPM
bodymap2_adrenal	0.23 RPM	629.54 RPM
bodymap2_brain	0.09 RPM	489.31 RPM
bodymap2_breast	0.06 RPM	490.86 RPM
bodymap2_colon	0.02 RPM	535.89 RPM
bodymap2_heart	0.04 RPM	269.31 RPM
bodymap2_kidney	0.15 RPM	464.01 RPM
bodymap2_liver	0.00 RPM	257.46 RPM
bodymap2_lung	0.09 RPM	592.28 RPM
bodymap2_lymph_node	0.05 RPM	446.35 RPM
bodymap2_ovary	0.25 RPM	648.99 RPM
bodymap2_prostate	0.09 RPM	490.85 RPM
bodymap2_skeletal_muscle	0.07 RPM	283.35 RPM
bodymap2_testis	0.17 RPM	574.25 RPM
bodymap2_thyroid	0.40 RPM	702.41 RPM
bodymap2_white_blood_cells	0.04 RPM	806.90 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2323 was not detected

EST

No EST(s) were mapped for retro_hsap_2323 retrocopy.

TSS

No TSS is located nearby retro_hsap_2323 retrocopy 5' end.

Lab

retro_hsap_2323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323 , retro_hsap_2674, retro_hsap_3385,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,