RetrogeneDB ID: retro_chof_406

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_104438:4540..5218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSCHOG00000013928
• Aliases: None
• Description: TRK-fused gene [Source:HGNC Symbol;Acc:11758]

Sequence

>retro_chof_406
TTGAGAAACCAAGATGAAATCAATAAAAATGACATGTCTGCATTTGGCTTAACAGGTGATCAGGTTTCAGGGCGACCAAG
TGCTCCTGCAGAAGACTGTTCAGGAATGCCCGAAAGCATTGCTTCTTCTTCCTCAGCAGCTCACCCATCAGGAGTTCAGC
CACAACACCCACCATATACAGGAGCTCAGACACAAGCAGGCAGATTGAAGGTCAGATTCAACAACAGTACCAGCAACAGG
CCGGCTATGGTGCCCAGCAACCACAAGCTCCCCCTCAGCCAGCACAACAGTATGGTATTCAGTATTCAGCAGGCTGTAGT
CAGCAGACTGGACCCCAGCAATCTCAGCAGTTCTGGGAATATGGCCAGCAGTCAACTTCCCAAGCACCGGCTCTTGCCTT
TTCTGGTCAGCCTCAACAACTGCCTGCTCAACTGCAGTACCAGGTGAGCAATTATCCTCCACCAACTTAAACCACCCAAA
CTTCTCAGCCTAATTACACTCTGGCCCCTACTTCACAACCTGGAAATGGCTCCAAGCCAACCCAGGGCCTATCAACCAAG
ACCAGGTTTCACTGCACCTCCTGTAAGTCCCATGACCCCTCCTCCAAGTGGACTTACCCCTTGTGCATGTAACTGTCCTC
CCTTCATTCAGGGCTATTCCCAACCTGGACTTGGCTAC

Alignment

ORF - retro_chof_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 67.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSGTPDSIASSSSAAHPPGVQPQQPPYTGAQTQAG-QI
          L.NQDEINKN.MSAFGLT.DQVSG.PSAPAED.SG.P.SIASSSSAAHP.GVQPQ.PPYTGAQTQAG.QI
Retrocopy LRNQDEINKNDMSAFGLTGDQVSGRPSAPAEDCSGMPESIASSSSAAHPSGVQPQHPPYTGAQTQAG<QI

Parental  EGQIYQQYQQQAGYGAQQPQAPPQPPQQYGIQYSAGYSQQTGPQQPQQFQGYGQQPTSQAPAPAFSGQPQ
          EGQI.QQYQQQAGYGAQQPQAPPQP.QQYGIQYSAG.SQQTGPQQ.QQF..YGQQ.TSQAPA.AFSGQPQ
Retrocopy EGQIQQQYQQQAGYGAQQPQAPPQPAQQYGIQYSAGCSQQTGPQQSQQFWEYGQQSTSQAPALAFSGQPQ

Parental  QLPAQTPQQYQASSYPPPTYTTQTSQPANYTVAPTSQPG-MTPSQPGAYQPRPGFTPPPGSTVTPPPSGP
          QLPAQ...QYQ.S.YPPPT.TTQTSQP.NYT.APTSQPG.M.PSQP.AYQPRPGFT.PP.S..TPPPSG.
Retrocopy QLPAQL--QYQVSNYPPPT*TTQTSQP-NYTLAPTSQPG>MAPSQPRAYQPRPGFTAPPVSPMTPPPSGL

Parental  NPYARNRLPFGQGYTQPGPGY
          .P.A.N..PF.QGY.QPG.GY
Retrocopy TPCACNCPPFIQGYSQPGLGY

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_406 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406 ,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,