RetrogeneDB ID: retro_chof_2064

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_47122:10036..10578(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSCHOG00000006219
• Aliases: None
• Description: general transcription factor IIH, polypeptide 3, 34kDa [Source:HGNC Symbol;Acc:4657]

Sequence

>retro_chof_2064
AAAGGGTAAAATACAGAGACTCTGCTGGCAGGGTCCCTTCCCAAAGCTCTTTGCTACATTCAGAGATTGAACAAAGAAGT
TAAAATTAATCAGGAAATAAAATCAAGGATATTGGTGATCAAGGCTGCAGAATACAGTGCATTGCCATACATGAACTTCA
TGAATGTAATTTTCGCTGCACAGAAACAGAGTATTTTGATCAATTCCTGTGTTTTAGACTCTGATTCAGTACTCCTCCAA
CAGGCTTGTGACATCACAGGGGGAGCTGTATTTGAAGGTGCCTCAGATGCCATCCCTTCTGCAGTATTTACTGTGGGTTT
TCCTTCCCAATCATGATCAGAGACCTCAGCTAATCCTGCTGCCCCCAATTCATGTAGACTACAGAGCTGCATGCTTCTGT
CATCACAATCTCATTGAAATTGGCTGTCTGTTCTGTGTGTTTGCCAATATTCTACAATTTCAGCCCTATCTGCACTACCT
GAGAGACAGCCTTTAAGATTTCTCGGCCTCCTGTACTGAAGGCCAAGAAAAAGAATCTGAAA

Alignment

ORF - retro_chof_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGQNTETLLAGSLAKALCXXXXXXXXXXXNQEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQNILIDAC
          KG.NTETLLAGSL.KALC...........NQE.KSRILVIKAAE.SAL.YMNFMNVIFAAQKQ.ILI..C
Retrocopy KG*NTETLLAGSLPKALCYIQRLNKEVKINQEIKSRILVIKAAEYSALPYMNFMNVIFAAQKQSILINSC

Parental  VLDSDSGLLQQACDITGG-LYLKV-QMPSLLQYLLWVFLPDHDQRSQLILPPPIHVDYRAACFCHRSLIE
          VLDSDS.LLQQACDITGG.LYLKV.QMPSLLQYLLWVFLP.HDQR.QLIL.PPIHVDYRAACFCH..LIE
Retrocopy VLDSDSVLLQQACDITGG>LYLKVPQMPSLLQYLLWVFLPNHDQRPQLILLPPIHVDYRAACFCHHNLIE

Parental  IGYVCSVCLSIFCSFSP-ICTTCETAFKISLPPVLKAKKKKLK
          IG....V...I...F.P.ICTT.ETAFKIS.PPVLKAKKK.LK
Retrocopy IGCLFCVFANIL-QFQP>ICTT*ETAFKISRPPVLKAKKKNLK

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_2064 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064 ,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550, retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357,