RetrogeneDB ID: retro_chof_2395

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_71252:3350..4026(+)
• 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_2395
GATGCAGAAAATGCAATTGTGCATACGGGAGGTCCATGGTTGTGTGGTCATCAGATCTGAACCAGTTGGGCCATGTGTAA
ACCACCTGCACCCAAAAGTACACAAGAAAACAACACTAAGCAGTTGAGATTTGAAGATGTAGTAAACCAGTCAAGTCCCA
AAAAATTGTACCATAAGCTGTGGAGGAATTGCTTCTGGGTTAACAGATCAGCTTATGAGTCAGACATTTTCACCATTTGG
ACAAATTATGGACATAAGAGTTTCTCCAGAGAAGGGCTATTCATTTGTCAGGTTTTCAACCCATGAAAGTGCAGCCCATG
CCATTGTTTCAGTGAATGGTACTACAATTGAAGGACATGTTAAACGTTATTGTGGTAAAGAATCTCCTGATATGACTAAC
AACTTCCAACATGTTCACTATAGTCAGTGGGGCCAGTGGAGCCAAGTTTATGGAAACTCACAATAATATAGACAGTATAT
GGCAAATAAGTGGCAAGTACTGCCTTATGGGGTGTATGGGCAACCATGGAATCAACAAGGATTTGCAGTAACTCAATCAC
CTTCTGCTGCTTGGATGGGTGGATTTGGTGCTCAGCCTCCCCAAGGACAAGACACTTCTCCTGTAATAACTCCTCCTAAC
AAAGGTGGATATGGTATGATGAGTTACCAAACACAG

Alignment

ORF - retro_chof_2395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.14 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DAENAIVHMGGQWLGGRQIRTNWATRKPPAPKSTQENNTKQLRFEDVVNQSSPK-NCTVYCGGIASGLTD
          DAENAIVH.GG.WL.G.QI.T.WA..KPPAPKSTQENNTKQLRFEDVVNQSSPK.NCT..CGGIASGLTD
Retrocopy DAENAIVHTGGPWLCGHQI*TSWAMCKPPAPKSTQENNTKQLRFEDVVNQSSPK>NCTISCGGIASGLTD

Parental  QLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTKNXXXV
          QLM.QTFSPFGQIM.IRV.PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHV.K.Y.GKESPDMT.N...V
Retrocopy QLMSQTFSPFGQIMDIRVSPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHV-KRYCGKESPDMTNNFQHV

Parental  DYSQWGQWSQVYGNPQQYGQYMANGWQVPPYGVYGQPWNQQGFGVDQSPSAAWMGGFGAQPPQGQAPPPV
          .YSQWGQWSQVYGN.Q.Y.QYMAN.WQV.PYGVYGQPWNQQGF.V.QSPSAAWMGGFGAQPPQGQ...PV
Retrocopy HYSQWGQWSQVYGNSQ*YRQYMANKWQVLPYGVYGQPWNQQGFAVTQSPSAAWMGGFGAQPPQGQDTSPV

Parental  IPPPNQAGYGMASYQTQ
          I.PPN..GYGM.SYQTQ
Retrocopy ITPPNKGGYGMMSYQTQ

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_2395 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,