RetrogeneDB ID: retro_ggor_1764

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:23309433..23310807(-)
• Located in intron of: ENSGGOG00000016862

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_1764
ATGGAAACTGAACAGCCAGAAGAAACCTTCCCTAACACTGAAACCAGTGGTGAATTTGGTAAACGCCCTGCAGAAGATAT
GGAAGAGGAACAAGCATTTAAAAGATCTAGAAACACTGATGAGATGGTTGAACTACCCATTCTGCTTCAGAGCAAGAATG
CTGGAGCAGTGACTGGAAAAGGAGGCAAGAATATTAAGGCTCTCCATACAGACTACAACGCCAGCATTTCAGTTCTAGAC
AGCAGTGGCCCACAGCGCATATTGCATATCAGTGCTGATATCGAAACAATTGGAGAAATTCTGAAGAAAATCATCACTAC
CTTGGAAGAGGGCCCACAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTGTGGAATACTTAA
ATTACCAACACTATAAAGGAAGGGACTTTGACTGCGAGTTGAGGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATTATT
GGGGTCAAAGGTGCTAAAATCAAAGAACTGAGAAAACACACAAACAACCATCACGCTTTTCCAGGAATGTTGTCCTCATT
TCACTGATAGAGTTGTTCTTATTGGAGGAAAACCCAATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATTTCT
GAGTCTCCCATCAAAGGACATGCACAGCCTTATGATCCCAATTTTTACGATGAAACCTATGATTATGGTGGTTTTACAAT
GGTGTTTGCTGACCACCGTGGACGCCCAGTGAGATTTCTGATGCGGGGAAGAGGTGGTTTTGACAAAATGTCTCCTGGTC
GGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGTTTATATGAGCCCTCGTCGAGGACCACCTCCCCCTCCTCCC
GGATGAGGTGGCCAGAGTGGTAGCAGAGCTCGGAATGTTCCTCTTCCTCCACCACCACCACCTAGGGGGGAGACCTCATG
ACCTATAACAGAAAAGGGAGACCTGGAAACCGTTACGACGGCGTGGTTGATTTCAGTGCTGATGAAACTTGGGGCTCTGC
AATAGATACATGGAACGCATCAGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCCAGATATGATTATTCCTATGCAG
GGTGTCATGGCTCATATGGTGATCTTGGTGGACCTATTATTACTACACAAGTAACTATTCCCAAAGATTTGGCTGGATCT
ATTATTGGCAAAGGTGGTCAGTGGATTAAACAAATCTGTCATGAGTAGGGAGCTTCGATCAAAATTGATGAGCCTTTAGA
AGGATCCGAAGATCGGATCATTACCATTACAGGAACACAGGACCAGATACAGAATGCACAGTATTTGCCGCAGAATAGTG
TGAAGCAGTATTCT

Alignment

ORF - retro_ggor_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

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

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYNAS.SV.DSSGP.RIL.ISADIETIGEILKKII.TLEEG.QLPSPTATSQLPLESDAVE.LNYQHYKG
Retrocopy DYNASISVLDSSGPQRILHISADIETIGEILKKIITTLEEGPQLPSPTATSQLPLESDAVEYLNYQHYKG

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

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          LDLISESPIKG.AQPYDPNFYDETYDYGGFTM.F.D.RGRPV.F.MRGRGGFD.M.PGRGGRPMPPSRRD
Retrocopy LDLISESPIKGHAQPYDPNFYDETYDYGGFTMVFADHRGRPVRFLMRGRGGFDKMSPGRGGRPMPPSRRD

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPR-GGDLMAYDRRGRPGDRYDGMVGFSADETWDSA
          Y..MSPRRGPPPPPPG.GG..GSRARN.PLPPPPPPR.GGDLM.Y.R.GRPG.RYDG.V.FSADETW.SA
Retrocopy YVYMSPRRGPPPPPPG*GGQSGSRARNVPLPPPPPPR<GGDLMTYNRKGRPGNRYDGVVDFSADETWGSA

Parental  IDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESG
          IDTW..SEWQMAYEPQGGS.YDYSYAG..GSYGDLGGPIITTQVTIPKDLAGSIIGKGGQ.IKQI.HE.G
Retrocopy IDTWNASEWQMAYEPQGGSRYDYSYAGCHGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQWIKQICHE*G

Parental  ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYA
          ASIKIDEPLEGSEDRIITITGTQDQIQNAQYL.QNSVKQY.
Retrocopy ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLPQNSVKQYS

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	0.14 RPM	254.83 RPM
SRP007412_cerebellum	0.08 RPM	240.25 RPM
SRP007412_heart	0.06 RPM	89.12 RPM
SRP007412_kidney	0.29 RPM	273.55 RPM
SRP007412_liver	0.13 RPM	223.10 RPM
SRP007412_testis	0.21 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_1764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1764 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,