RetrogeneDB ID: retro_chof_1723

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_36733:10114..10573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL1
• Ensembl ID: ENSCHOG00000010262
• Aliases: None
• Description: thioredoxin-like 1 [Source:HGNC Symbol;Acc:12436]

Sequence

>retro_chof_1723
GGACCATGTTTAAGGATCGCTCTAGCATTCAGTTCTATGAATAATAAATACCCACAGGCAGTTTTCTTGGAGGTGGATGT
GCATCAGTGTCAGGGAACAGCTGCCACCAATAATATCTCAGCAACACCTGCATTTCTATTTTTTCGAAACAAAGTGAGAA
TTGACCAATATCAAGGAGTAGATGCTGTGCGATTAGAAGAAAAAATTAAACAGCACCTAGAAAATGACCCTGGAAGCAAT
GAGGACACAAACATTCCAAAAGGCTATATGGATTTAATGCCTTTTATTAACAAAGCTGGCTGTGAATGTCTTAATGAGAG
TGATGAACATGGATTTGACAACTGTTTACGAAAAGACATGACCTTCTTGGAGTCTGACTGTGATGAACAGCTCCTTATTA
CCGTGGCATTCAATCAACCTATTAAGCTTTATTCCATGAAATTTCAAGGGCCAGATAAT

Alignment

ORF - retro_chof_1723 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 59.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPCLRIAPAFSSMSNKYPQAVFLEVDVHQCQGTAATNNISATPTFLFFRNKVRIDQYQGADAVGLEEKIK
          GPCLRIA.AFSSM.NKYPQAVFLEVDVHQCQGTAATNNISATP.FLFFRNKVRIDQYQG.DAV.LEEKIK
Retrocopy GPCLRIALAFSSMNNKYPQAVFLEVDVHQCQGTAATNNISATPAFLFFRNKVRIDQYQGVDAVRLEEKIK

Parental  LHLENDSGSSXXXXXXXXXMDLMPFINKAGCECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQP
          .HLEND.GS..........MDLMPFINKAGCECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQP
Retrocopy QHLENDPGSNEDTNIPKGYMDLMPFINKAGCECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQP

Parental  VKLYSMKFQGPDN
          .KLYSMKFQGPDN
Retrocopy IKLYSMKFQGPDN

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_1723 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 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000137	1 retrocopy	retro_cfam_875,
Choloepus hoffmanni	ENSCHOG00000010262	1 retrocopy	retro_chof_1723 ,
Choloepus hoffmanni	ENSCHOG00000011506	10 retrocopies	retro_chof_1111, retro_chof_127, retro_chof_1557, retro_chof_1680, retro_chof_1696, retro_chof_240, retro_chof_2424, retro_chof_317, retro_chof_617, retro_chof_82,
Ictidomys tridecemlineatus	ENSSTOG00000000075	2 retrocopies	retro_itri_302, retro_itri_414,
Tupaia belangeri	ENSTBEG00000017328	2 retrocopies	retro_tbel_1981, retro_tbel_911,
Tursiops truncatus	ENSTTRG00000001161	1 retrocopy	retro_ttru_1154,