RetrogeneDB ID: retro_chof_670

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_133482:4251..4927(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIAL1
• Ensembl ID: ENSCHOG00000009888
• Aliases: None
• Description: TIA1 cytotoxic granule-associated RNA binding protein-like 1 [Source:HGNC Symbol;Acc:11804]

Sequence

>retro_chof_670
GATGCAGAAAATGCAATTGTGCATATGGGAGGTCAGTGGTTGGGTGGTCATCAGATCCGAACCAATTGGGCCACACGTAA
ACCACCTGCACCTAAAAGTACACAAGAAAACAACACTTAGCAGTTGAGATTTGAAGATGTAGTAAACCAGTCAAGTCCAA
AAAATTGTACTGTATACTGTGGAGGAATTGCTTCTGGGTTAACAGATCAGTTTATGAGACAGATGTTTTCACCATTTGGA
CAAATTATGGAAATAAGTTTTTCCAGAGAAGGGCTATTCATTTGTCAGGTTTTCAACCCATGAAAGTGCAGTCCATGCCA
TTGTTTCAGTGAACGACACTACAATTGAAGGACATGTTGTTAAATGCTATTGGGGTAAACAATCTCCTGATATGACTAAA
AACTTCCTACAGGTTGACTATATTCTGTGGGGCCAATGGAGCAAGTTTATGGAAACCCACAGCAGTACAGACCGTATATG
GCAAATGGGTGGCAAGTACCGCCTTATGGGGGTGTATGGGCAACCATGGAATCAACAAGGATTTGGAGTACATCTATCAC
CTTCTGCTGCTTGGATGGGTGGATTTGGTGCTCACCCTCCCCAAGGACAAGCCCCTCCCCCTGTAATACCTCCTCCTAAC
CAAGCTGGATATGGTATGGCAAGTTACCAAACACAG

Alignment

ORF - retro_chof_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DAENAIVHMGGQWLGGRQIRTNWATRKPPAPKSTQENNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQ
          DAENAIVHMGGQWLGG.QIRTNWATRKPPAPKSTQENNT.QLRFEDVVNQSSPKNCTVYCGGIASGLTDQ
Retrocopy DAENAIVHMGGQWLGGHQIRTNWATRKPPAPKSTQENNT*QLRFEDVVNQSSPKNCTVYCGGIASGLTDQ

Parental  LMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTKNXXXV
          .MRQ.FSPFGQIMEI..F...G.YSFVRFSTHESA.HAIVSVN.TTIEGHVVKCYWGK.SPDMTKN...V
Retrocopy FMRQMFSPFGQIMEIS-FSREG>YSFVRFSTHESAVHAIVSVNDTTIEGHVVKCYWGKQSPDMTKNFLQV

Parental  DYSQWGQWS-QVYGNPQQYGQYMANGWQVPPY-GVYGQPWNQQGFGVDQSPSAAWMGGFGAQPPQGQAPP
          DY..WGQWS.QVYGNPQQY..YMANGWQVPPY.GVYGQPWNQQGFGV..SPSAAWMGGFGA.PPQGQAPP
Retrocopy DYILWGQWS<QVYGNPQQYRPYMANGWQVPPY>GVYGQPWNQQGFGVHLSPSAAWMGGFGAHPPQGQAPP

Parental  PVIPPPNQAGYGMASYQTQ
          PVIPPPNQAGYGMASYQTQ
Retrocopy PVIPPPNQAGYGMASYQTQ

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_670 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009888	2 retrocopies	retro_chof_2395, retro_chof_670 ,
Oryctolagus cuniculus	ENSOCUG00000003783	1 retrocopy	retro_ocun_904,
Rattus norvegicus	ENSRNOG00000020271	1 retrocopy	retro_rnor_2547,
Sus scrofa	ENSSSCG00000010685	1 retrocopy	retro_sscr_11,