RetrogeneDB ID: retro_chof_2117

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_50947:8695..9986(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCC1
• Ensembl ID: ENSCHOG00000002988
• Aliases: None
• Description: transmembrane and coiled-coil domain family 1 [Source:HGNC Symbol;Acc:29116]

Sequence

>retro_chof_2117
GGAATTCAGATGGCAGCTGTTATGCAGTCAGGCCGGCTCAGGTCTTCATCCACGACAGATGCTCCTAGCGGCTCAGCTGT
GATGGAAATAGCTTGTGCTGCTGCTGCATGTCTGCCAGGATAGGAGGCAACTGCAGAGCAGACCAAGTGGTTGGAAGCAA
GCAGCCTTGCCCACACTTCCAGTGCAGTGGCTTCTAGCACTGATGGCAGCATCCACACAGACTCCATGAGTGGAACACCA
GACCCTCAGCATACAAAGGCTGCTATTGCTCACCTGCAGCAGAAGATCCCGAAGCTTCCAGAACAGATCACGATTGCACA
AACAGCTCGGGACAACAATGTTGCTGAGTACTTGAAGCTTGCCAACAGCGCAGACAAGCAGCCAGCAGCCTGCATCACAC
AGGTCTTTGAGAAGAAGAACCAGAAATCCTCCCAACCATCCTCCAGCTACAAAAGAAGCTTGAGCACTACCACCAGAAGC
TCTGGGAGGTAGAACAGAATGGGGTGCTATGGCAGTGAAGAGATGTCTTCTGGGATGTGCACCAAGGTCTGAAGGATGTG
GGAGCAAAGGGACTGGCTTCAGTGAGGTTGTGGTGGACAGCGTCGAGGGTGGACTCTCCAGTTTCTCCCAGGCCACCCCT
TCAGCAGCAGGGGCTGTGGTCTCAAAACCCAGAGAGACCGCCTCAGTGATTCGGAATAAATTTGACAGTGCAGACAACAT
CTCTAATCTGAAAGACTACTTAGAGGAAGGGCTAGTGGAGGATGGGGGAAGATTTTGGGGGTGATTTCAAACTTTCAAAT
GAGTCAAAATGTGGTAGTGAGGAAGATTGTTCAAGTGCCACATCAGGCTCAGTGGGAGCCAACAGCATGACTGGGGCATT
GCTGTAGGAGCATCCAGCTCCAAAACAAACACCGTGGACATGCAGAGCTCAGGATTTAATCCACATGAGATCCAGGAGAT
CTGGGAAACCCAGGCCAGGCTAGAGGAATCCTTTGGGACCCTCAAGGAACATTGTCAGAGGGACTATTCCTTAATTATGC
AGTTCTTACAGGAGGAGTGATATAGGTGTGAACGATTAGAAGAACAGCTAAATGACTTAACAGAGCTCCACCAGCATTAC
ATCGTGAACTTGAAGCAAGAATTGGCCAGCATGGAAGAGAGAAATCGCAATGAACAGACCCAAGACATTCAGGAGGTCCT
GGAGGCGTGCCTGACCCGCATCTCCAAGATGAAACTCGAGCAGCAGCAGCAGCAGGTGACGCAGCTGGAAGGGCTGAACA
ATGCAGAAGCC

Alignment

ORF - retro_chof_2117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.53 %
• Parental protein coverage: 67.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GQEMAAVMQSGRPRSSSTTDAPSSSAVIEIACAAAAAACLPGEEATAERIERLEVSSLAHTSSAVASSTD
          G..MAAVMQSGR.RSSSTTDAPS.SAV.EIACAAAA..CLPG.EATAE....LE.SSLAHTSSAVASSTD
Retrocopy GIQMAAVMQSGRLRSSSTTDAPSGSAVMEIACAAAA--CLPG*EATAEQTKWLEASSLAHTSSAVASSTD

Parental  GSIHTDSVDGTPDPQRTKAAIAHLQQKILKLTEQIKIAQTARDDNVAEYLKLANSADKQQAARIKQVFEK
          GSIHTDS..GTPDPQ.TKAAIAHLQQKI.KL.EQI.IAQTARD.NVAEYLKLANSADKQ.AA.I.QVFEK
Retrocopy GSIHTDSMSGTPDPQHTKAAIAHLQQKIPKLPEQITIAQTARDNNVAEYLKLANSADKQPAACITQVFEK

Parental  KNQKSSQ-TILQLQKKLEHYHRKLREVEQNGIPRQPKDVFRDMHQGLKDVGA-KVTGFSEGVVDSVKGGL
          KNQKSSQ.TILQLQKKLEHYH.KL.EVEQNG...Q..DVF.D.HQGLKDVGA.K.TGFSE.VVDSV.GGL
Retrocopy KNQKSSQ<TILQLQKKLEHYHQKLWEVEQNGVLWQ*RDVFWDVHQGLKDVGA<KGTGFSEVVVDSVEGGL

Parental  SSFSQATHSAAGAVVSKPREIASLIRNKFGSADNISNLKDSLEEGQVEDG-GKTLGVISNFQSS-PKYGS
          SSFSQAT.SAAGAVVSKPRE.AS.IRNKF.SADNISNLKD.LEEG.VEDG.GK.LGVISNFQ.S..K.GS
Retrocopy SSFSQATPSAAGAVVSKPRETASVIRNKFDSADNISNLKDYLEEGLVEDG<GKILGVISNFQMS<SKCGS

Parental  EEDCSSATSGSVGANSTTG-GIAVGASSSKTNTLDMQSSGFDALLHEIQEIRETQARLEESFETLKEHYQ
          EEDCSSATSGSVGANS.TG.GIAVGASSSKTNT.DMQSSGF....HEIQEI.ETQARLEESF.TLKEH.Q
Retrocopy EEDCSSATSGSVGANSMTG<GIAVGASSSKTNTVDMQSSGFNP--HEIQEIWETQARLEESFGTLKEHCQ

Parental  RDYSLIMQTLQEERYRCERLEEQLNDLTELHQNEILNLKQELASMEEKIAYQSYERARDIQEALEACQTR
          RDYSLIMQ.LQEE.YRCERLEEQLNDLTELHQ..I.NLKQELASMEE.......E...DIQE.LEAC.TR
Retrocopy RDYSLIMQFLQEE*YRCERLEEQLNDLTELHQHYIVNLKQELASMEER---NRNEQTQDIQEVLEACLTR

Parental  ISKMELQQQQQQVVQ-EGLENATA
          ISKM.L.QQQQQV.Q.EGL.NA.A
Retrocopy ISKMKLEQQQQQVTQLEGLNNAEA

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_2117 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002988	2 retrocopies	retro_chof_1711, retro_chof_2117 ,