RetrogeneDB ID: retro_pabe_2105

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:25160871..25161634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSPPYG00000019327
• Aliases: HNRNPK, HNRPK
• Description: Heterogeneous nuclear ribonucleoprotein K [Source:UniProtKB/Swiss-Prot;Acc:Q5R5H8]

Sequence

>retro_pabe_2105
AAGATCATCTTTGATATTATTTTCTCAGTCTCCCCATCAAAAGGACAAGCACAGCGTTATGATCCCAATTCTTACCAATG
AAACCTATGATTATGGTGGTTTTATAATAGTGTTTGCTGACCACCGTGGACGCCCAGTGAGATTTCTCATGCGGGGAAGA
GGTGGTTTTGACAAAATGTCTCCTGGTCGGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGTTTATATGAGCCC
TCGTCGAGGACCACCTCCCCCTCCTCCCAGATGAGGTGGCCAGAGTGGTAGCAGAGCTCAGAATGTTCCTCTTCCTCCAC
CACCACCACCTAGAGGGGGAGACCTCATGACCTATAACAGAAAAGGGAGACCTGGAAACCGTTACGACGGCGTGGTTGAT
TTCAGTGCTGATGAAACTTGGGACTCCGCAATAGATACACGGAACACATCAGAATGGCAGATGGCTTATGAACCACAGGG
TGGCTCCAGATATGATTATTCCTATGCAGGAGGTCATGGCTCATAAGCTGATCTTGGTGGACCCATTATTACTACACAAG
TAACTATTCCCAAAGATTTGGCTGCATCTATTATTGGCAAAGGTGGTCAGTGGATTAAACAAATCTGTCATGAGTAGGGA
GCTTCGATCGAAATTGATGAGCCTTCAGAAGGATCCGAAGATTGGATCATTACCATTACAAGAACACAGGACCAGATACA
GAATGCACAGTATTTGCTGCAGAATAGTGTGAAGCAGTATTCT

Alignment

ORF - retro_pabe_2105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.78 %
• Parental protein coverage: 54.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KIILDLI-SESPIKGRAQPYDPNFY-DETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMP
          KII.D.I.S.SP.KG.AQ.YDPN.Y..ETYDYGGF...F.D.RGRPV.F.MRGRGGFD.M.PGRGGRPMP
Retrocopy KIIFDIIFSVSPSKGQAQRYDPNSY>NETYDYGGFIIVFADHRGRPVRFLMRGRGGFDKMSPGRGGRPMP

Parental  PSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADET
          PSRRDY..MSPRRGPPPPPP..GG..GSRA.N.PLPPPPPPRGGDLM.Y.R.GRPG.RYDG.V.FSADET
Retrocopy PSRRDYVYMSPRRGPPPPPPR*GGQSGSRAQNVPLPPPPPPRGGDLMTYNRKGRPGNRYDGVVDFSADET

Parental  WDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIR
          WDSAIDT...SEWQMAYEPQGGS.YDYSYAGG.GS..DLGGPIITTQVTIPKDLA.SIIGKGGQ.IKQI.
Retrocopy WDSAIDTRNTSEWQMAYEPQGGSRYDYSYAGGHGS*ADLGGPIITTQVTIPKDLAASIIGKGGQWIKQIC

Parental  HESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYA
          HE.GASI.IDEP.EGSED.IITIT.TQDQIQNAQYLLQNSVKQY.
Retrocopy HE*GASIEIDEPSEGSEDWIITITRTQDQIQNAQYLLQNSVKQYS

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	279.55 RPM
SRP007412_cerebellum	0.00 RPM	257.55 RPM
SRP007412_heart	0.00 RPM	133.15 RPM
SRP007412_kidney	0.07 RPM	269.95 RPM
SRP007412_liver	0.00 RPM	212.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2105 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2105 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
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,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105 , retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
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,