RetrogeneDB ID: retro_chof_1428

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_292164:305..1065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARPBP
• Ensembl ID: ENSCHOG00000011914
• Aliases: None
• Description: PARP1 binding protein [Source:HGNC Symbol;Acc:26074]

Sequence

>retro_chof_1428
ATGGATGTCATTGACCACTATGAGGAAATCAGGAAGAACTATGATGATTTTTTGAAGAATAGTAATATGTTAGATCTGAT
TGATGTTTATCAAAAATATAGGGTTTTGAGTTCTAGTTGTGAAAAGGATGACAGTATAACCCTAGTCAACTATGGGATTT
TCTATCTGGCAGACAGTGTGCAGTAAATAATGAAACCTATCTTTATGTACCAACATCACCACAAGTAGGCACAATGAGGA
TAATGAAAAGGTGCAGTTACTAGCAAAGAAAATTATCTATTCATATTTAAACCTGCTATTGAATTCAAAGAATGACTTGA
CTTTGGCTCATATTTTCAATATCCCTGATAGGCAACTTGGAAGAGAAGCCTCTACAGACTTGAAACATGCTGCTCCAGAG
AAACAGATGTCTGTCTTTTTGGTGGCCACATCATTCATTTGCAAAATACAGCTTGGAGGAAAAGGATATGCACCATTGCC
ATCTGATCCTTTAAGGACACATGTAAAGGGAATTTCTAATTTTATTAATTTTGTTGACAAGTTAGATGAGATTCTTGGAG
AAATACCAAATTCAAGCATTGCAGGAGGTTGGACACTGTGATTGATAAAGATGCAACTGATTAAAAGCCAGGACAGCAGT
GATCCTTTTTATAAAGCAGTAGAAGAAGTTGCTAAGGATTTGGATTTGAGGATTAAAAATATCATCTATTTTCAACAAGA
ACTTGTAGTTGTTTGCATCACTGATATCAGTCCTGCAAGG

Alignment

ORF - retro_chof_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.17 %
• Parental protein coverage: 50.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEVIDHYEEIRKTYDDFLKNSNMVDLIDVYQKYGVLTSSCEKDDNIS-PSQLRDFLSGRQYAVNDETDLC
          M.VIDHYEEIRK.YDDFLKNSNM.DLIDVYQKY.VL.SSCEKDD.I..PSQL.DFLSGRQ.AVN.ET.L.
Retrocopy MDVIDHYEEIRKNYDDFLKNSNMLDLIDVYQKYRVLSSSCEKDDSIT<PSQLWDFLSGRQCAVNNETYLY

Parental  VPTSP-TSKHNEDNGKVQLLAKKIIYSYLNLLVNSKNDLALARILNIPDRGLGRKAFTDLKHAAREKQMS
          VPTSP.TS.HNEDN.KVQLLAKKIIYSYLNLL.NSKNDL.LA.I.NIPDR.LGR.A.TDLKHAA.EKQMS
Retrocopy VPTSP<TSRHNEDNEKVQLLAKKIIYSYLNLLLNSKNDLTLAHIFNIPDRQLGREASTDLKHAAPEKQMS

Parental  IFLVATSFIRTIELGGKGYAPSPSDPLRAHIKGLSNFINFVDKLDEILGEIPNPSIAGSRILSEIKMQMI
          .FLVATSFI..I.LGGKGYAP.PSDPLR.H.KG.SNFINFVDKLDEILGEIPN.SIAG...L..IKMQ.I
Retrocopy VFLVATSFICKIQLGGKGYAPLPSDPLRTHVKGISNFINFVDKLDEILGEIPNSSIAGGWTL*LIKMQLI

Parental  KGQTSRDPLYNAVVEVVQE-EMWIKNILYSHQGVVAVSTTDISRAR
          K.Q.S.DP.Y.AV.EV.......IKNI.Y..Q..V.V..TDIS.AR
Retrocopy KSQDSSDPFYKAVEEVAKDLDLRIKNIIYFQQELVVVCITDISPAR

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_1428 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011914	1 retrocopy	retro_chof_1428 ,
Tupaia belangeri	ENSTBEG00000013476	1 retrocopy	retro_tbel_3666,