RetrogeneDB ID: retro_chof_1023

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_18502:420..1800(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSCHOG00000010832
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_chof_1023
ATGGAAACTGAACAGCCAGAGGAAACCTTCCCCAACACGGAAACCAATGGTGAATTTGGTAAACGTCCTGCAGAAGATAT
GGAAGAGGAACAAGCGTTTAAAAGATCTAGAAATGTGGATGAGATGTTGGAGCGTTGCATTCTGCTTCAGAGCAAAAATG
CTGGGACAGTGATTGGAGAAGGAGGCAAGAATATTAAGGCCCTCCATACAGACTACAATGCCAGTGTTTCAGTACCAGAC
AGCAGTGGCCCCGAGCGCATATTGAGTATCAGTGCTGATATTGAGACAATTGGAGAAATTCTGAAGAAAATCATCCCTAC
CTTGGAAGAGGGCCTGCAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTGTGGAATGCTTAA
ATTACCAACACTATAAAGGAAGCGACTTTGACTGCGAGTTGAGACTGTTGATTCATCAGAGTCTGGCAGGAGGAACTATT
GGGGTCAAGGGTGCTAAAATCAAAGAACTTTGAGAGAATACTCAGACAACAATCAAGCTTTTCCAGGAATGCTGTCCTCA
TTCCACTGACAGGGTCATCTTTATTGGAGGAAAGCCTGATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATAT
CTGAGTCTCCCATCAAAGGATGTGCAAAGCCTTATGATCCCAATCTTTATGATGAAACTTATGATTATGGTAGTTTTATG
ATGATGTTTGATGACCGCCGTGGACGTCCTGTGGGATTTCCCATGCAGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGG
TCGGGGTGGGCGTCCAATGCCTCCATCCAGAAGAAACTAATATGAGTGCTCCTTGAGAACGAGGACCTCCTCCTCCTGGA
CGAGGTGGCTGGGATGGCAGCAGAGCTCAGAATCTTTGTCTTCCACCACCACCACCACCACCACCACCTAGAGGAGGAGC
TCTAATGGCTTATCTCAGAAGGAGAAGACCTGGAGACCGTTATGATGGCATGGTTGGTTTCAGTGCTGATGAAACTTGGG
ACTCTGCAGTAGATACATGGAGCCCATCAGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCTGGATATGATTATTCC
TATGCAGGGGGTTATGGCTCATATGGTGATCTCAGTGGACCTATTATTACTGCACAAGTAACTATTCCCAAAGATTTGGC
TGGATCTACAATTGGGAAAGGTGGTCAGCAGATTAAACAAATCTGTCATGAGTTGAGAGTTTCAATCAAAAATAAGGAAC
CTTTAGAAGGTTCCAAAGATCAGATCGTTACCATTACAGAGACACACAACTGCATACAGAATGCACAGTATTTGCTGCAG
AACAGTTGAAGCAGTATTCT

Alignment

ORF - retro_chof_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
          METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRN.DEM.E..ILLQSKNAG.VIG.GGKNIKAL.T
Retrocopy METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNVDEMLERCILLQSKNAGTVIGEGGKNIKALHT

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
Retrocopy DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG

Parental  SDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIIL
          SDFDCELRLLIHQSLAGG.IGVKGAKIKEL.ENTQTTIKLFQECCPHSTDRV..IGGKPDRVVECIKIIL
Retrocopy SDFDCELRLLIHQSLAGGTIGVKGAKIKEL*ENTQTTIKLFQECCPHSTDRVIFIGGKPDRVVECIKIIL

Parental  DLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDY
          DLISESPIKG.A.PYDPN.YDETYDYG.F.MMFDDRRGRPVGFPM.GRGGFDRMPPGRGGRPMPPSRR..
Retrocopy DLISESPIKGCAKPYDPNLYDETYDYGSFMMMFDDRRGRPVGFPMQGRGGFDRMPPGRGGRPMPPSRRN*

Parental  DDMSPR-RGP-PPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSA
          ...S.R.RGP.PP...G..G.................RGG.LMAY.RR.RPGDRYDGMVGFSADETWDSA
Retrocopy YECSLR>RGPPPPGRGGWDGSRAQNLCLXXXXXXXXXRGGALMAYLRRRRPGDRYDGMVGFSADETWDSA

Parental  IDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESG
          .DTWSPSEWQMAYEPQGGSGYDYSYAGG.GSYGDL.GPIIT.QVTIPKDLAGS.IGKGGQ.IKQI.HE..
Retrocopy VDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLSGPIITAQVTIPKDLAGSTIGKGGQQIKQICHELR

Parental  ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNS-VKQYA
          .SIK..EPLEGS.D.I.TIT.T...IQNAQYLLQNS..KQY.
Retrocopy VSIKNKEPLEGSKDQIVTITETHNCIQNAQYLLQNS<LKQYS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023 , retro_chof_1589,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
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,