RetrogeneDB ID: retro_chof_1589

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_332774:13..747(+)
• 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_1589
GTGGTGGAATTCCCCATCAAAGGACATGTGCAGCCTTATGATCCCAATTTTTATGATGAAACCTATGATTACGATGGTTT
TACAATGATGTTTGATGACCGCTGTGGATGTTCTGTGGGATTTCCCATGCAGGAAAGAGATGGTTTTCACCGAATGCCTC
CTGGTCAGGGTGGGCATCCAATGCCTCCATCTAGAAGAGATTATGATGATATGAGCCCTCGTCAAGGACCTCCTCCTCCT
CCTCCTCCTGGACAAGGTGGCTGGGGTGGCAGCAGAGCTCAGAATCTTCCTCTTCCTCCACCACGACCACCTAGAGGAGG
AGATCTAATGGCTTATGACAGAAGAGGAAGACCTGGAAACCATTATGATAGTTTCAGTGCTGATGAAACTTGGGATTCTG
CAATAGATACATGGAGCCCATCACAATGGCAGATGGCTTATGAACCACAGGGTGGCTCTGGATATGATTATTTCTATGCA
GGGGGTTGTGGCTCATATGGTGATCTTGGTGGACCTATTATTACTACATAAGTAACTATTCTCAAAGATTTGGCTGGATC
TATTATTGGGACAGGTGGTCAGTGGATTAAACAAATCCATCATGAGTCGGGAGCTCAATCAAAATTGATGAACCTTTAGA
AGGATCCGAAGATTGGATCATTACCATTACAGGAACACAGGACCAGATACAGAATGCACAGTATTTGTTGCAGAACAGTG
TGAAGCAGTATTCT

Alignment

ORF - retro_chof_1589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.33 %
• Parental protein coverage: 53.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDD
          ..E.PIKG..QPYDPNFYDETYDY.GFTMMFDDR.G..VGFPM..R.GF.RMPPG.GG.PMPPSRRDYDD
Retrocopy VVEFPIKGHVQPYDPNFYDETYDYDGFTMMFDDRCGCSVGFPMQERDGFHRMPPGQGGHPMPPSRRDYDD

Parental  MSPRRG-PPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDT
          MSPR.G.......G.GG.GGSRA.NLPLPPP.PPRGGDLMAYDRRGRPG..YD....FSADETWDSAIDT
Retrocopy MSPRQGXXXXXXXGQGGWGGSRAQNLPLPPPRPPRGGDLMAYDRRGRPGNHYD---SFSADETWDSAIDT

Parental  WSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA-S
          WSPS.WQMAYEPQGGSGYDY.YAGG.GSYGDLGGPIITT.VTI.KDLAGSIIG.GGQ.IKQI.HESGA.S
Retrocopy WSPSQWQMAYEPQGGSGYDYFYAGGCGSYGDLGGPIITT*VTILKDLAGSIIGTGGQWIKQIHHESGA<S

Parental  IKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYA
          IKIDEPLEGSED.IITITGTQDQIQNAQYLLQNSVKQY.
Retrocopy IKIDEPLEGSEDWIITITGTQDQIQNAQYLLQNSVKQYS

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_1589 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,