RetrogeneDB ID: retro_ggor_1866

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:95348352..95349740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSGGOG00000015500
• Aliases: None
• Description: None

Sequence

>retro_ggor_1866
ATGTAAACTGAACAGCCGGAAGAAACCTTCCCGAACACTGAAACCAATGGTGAATTTGGTAAACACCCTGCAGAAGATTT
GGAAGAGTAACAAGCATTTAAAAGATCTAGAAACACTGATGAGATGGTTGAATTACGCATTCTGCTTCAGAGCAAGAATG
CTGGGGCAGTGATTGAAAAAGGAGGCAAGAATATCAAGGCTCTCCGTACAGACTACAATGCCAGTGTTTCAGTCCCAGAC
AGCAGTGGCCCCGAGCACATATTGAGCATCAGTGCTGGTATTGACACAATTGGAGAAATTCTGAAGAAAATCATCCCTGC
CTTGGAAGAGGGCCTGCAGTTTCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGTTGCTGTGGAATGCTTAA
ATTACCAACACTATAAAGGAAGTGACTTTGACTGCGAGTTGAGGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATTATT
GGGGTCAAAGGTGCTAAAATCAAAGAACTTCGAGAGAACACTCAAACCACCATCAAGCTTTTCCAGGAATGCTGTCCTCA
TTCCACTGACGAGTTGTTCTTATTGGAGGAAAACCCGATGGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATATA
TGAGTCTCCCATCAAAGGACGTGCACAGCCTTATGATCCCAAATTTTATGATGAAACCTATGATTATGGTGGTTTTACAA
TTATGTCTGATGACCGCTGTGGACGCCCAGTGGGATTTCCCATGCGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGGT
CAGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGATGATATGAGCCCTGGTCGAGGACCACCTCCACCTCCTCC
CGGACAAGGCTGCCAGGGTGGTAGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGGGGGAGACCTCA
TGGCCTATGACAGAAGAGGGAGACCTGGAGACTGTTACAATGGCATGGTTGGTTTCAGTGCTGATGAAACTTGGGACTCT
GCAATAGATACATGGAGCCCATCAGAATGTTAGATGGCTTATGAACCACAGGGTGGCTCCAGATATGATTATTCCTATGC
AGGGGGTCGTGGCTCATATGGTGATCTTGGTGGACTTATTATTACTACACAAGTAACGATTCCCAAAGATTTGGCTGGAT
CTGTTATTGGCAAAGGTGGTCTGCAGATTAAACAAATCCGTCATGAGTCGGGAGCTTCGATCAAAATTGATGAGCCTTTA
GAAGGATTGAAAGATTGGATCATTACCATTACAGGAACACAGGACCAGATACAGAATGCACAGTATTTGCTGCAGAACAG
TGTGAAGCAGTATGCAGATGTTGAAGGA

Alignment

ORF - retro_ggor_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.46 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
          M.TEQPEETFPNTETNGEFGK.PAED.EE.QAFKRSRNTDEMVELRILLQSKNAGAVI.KGGKNIKALRT
Retrocopy M*TEQPEETFPNTETNGEFGKHPAEDLEE*QAFKRSRNTDEMVELRILLQSKNAGAVIEKGGKNIKALRT

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYNASVSVPDSSGPE.ILSISA.I.TIGEILKKIIP.LEEGLQ.PSPTATSQLPLES.AVECLNYQHYKG
Retrocopy DYNASVSVPDSSGPEHILSISAGIDTIGEILKKIIPALEEGLQFPSPTATSQLPLESVAVECLNYQHYKG

Parental  SDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTD-RVVLIGGKPDRVVECIKII
          SDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTD.RVVLIGGKPD.VVECIKII
Retrocopy SDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTD<RVVLIGGKPDGVVECIKII

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          LDLI.ESPIKGRAQPYDP.FYDETYDYGGFT.M.DDR.GRPVGFPMRGRGGFDRMPPG.GGRPMPPSRRD
Retrocopy LDLIYESPIKGRAQPYDPKFYDETYDYGGFTIMSDDRCGRPVGFPMRGRGGFDRMPPGQGGRPMPPSRRD

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAI
          YDDMSP.RGPPPPPPG.G..GGSRARNLPLPPPPPPRGGDLMAYDRRGRPGD.Y.GMVGFSADETWDSAI
Retrocopy YDDMSPGRGPPPPPPGQGCQGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDCYNGMVGFSADETWDSAI

Parental  DTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA
          DTWSPSE..MAYEPQGGS.YDYSYAGGRGSYGDLGG.IITTQVTIPKDLAGS.IGKGG..IKQIRHESGA
Retrocopy DTWSPSEC*MAYEPQGGSRYDYSYAGGRGSYGDLGGLIITTQVTIPKDLAGSVIGKGGLQIKQIRHESGA

Parental  SIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYADVEG
          SIKIDEPLEG..D.IITITGTQDQIQNAQYLLQNSVKQYADVEG
Retrocopy SIKIDEPLEGLKDWIITITGTQDQIQNAQYLLQNSVKQYADVEG

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	0.82 RPM	254.83 RPM
SRP007412_cerebellum	0.83 RPM	240.25 RPM
SRP007412_heart	0.28 RPM	89.12 RPM
SRP007412_kidney	0.90 RPM	273.55 RPM
SRP007412_liver	0.69 RPM	223.10 RPM
SRP007412_testis	1.24 RPM	375.45 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023, retro_chof_1589,
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,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866 ,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
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,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
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,