RetrogeneDB ID: retro_chof_1711

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_36511:11348..12791(+)
• 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_1711
CAGAGGCCAGAAAGCAGACAGAATCTGAACAAAAGTTGTCTGCAATGACCCACTAATGTAAATGGCCAAGCCTGAAGCAG
CTCTTCCAGCACCAGCACAGCAGGTCATCAGTGTCTCCACATGGTGCACAGCAAATTCAGGCAGAGTCAGAACCTGAAAT
GGATGTGGAGAGCCAGAACACAGGTGCTGAGATTGACTCTGTCTCCACCCACCCCACAGCTCTGAATCGACTTCTGCAGC
AGATCCAAGTGCCTCTCAAGATGAAGAGAGGGACGAGTTTGCATAGTAGATGGGGCAAGCCAGAAGCCCCAAAGGGAAGT
CCCCAAGTCAACAGGAGATCTGGCCAGGAGATGGCAGCTGTTATGCAGTCAGGCCGGCTCAGGTCTTCATCCACGACAGA
TGCTCCTAGCGGCTCAGCTGTGATGGAAATAGCTTGTGCTGCTGCTGCATGTCTGCCAGGATAGGAGGCAACTGCAGAGC
AGACCAAGTGGTTGGAAGCAAGCAGCCTTGCCCACACTTCCAGTGCAGTGGCTTCTAGCACTGATGGCAGCATCCACACA
GACTCCATGAGTGGAACACCAGACCCTCAGCATACAAAGGCTGCTATTGCTCACCTGCAGCAGAAGATCCCGAAGCTTCC
AGAACAGATCACGATTGCACAAACAGCTCGGGACAACAATGTTGTTGAGTACTTGAAGCTTGCCAACAGCGCAGACAAGC
AGCCAGCAGCCTGCATCACACAGGTCTTTGAGAAGAAGAACCAGAAATCCTCCCAACCATCCTCCAGCTACAAAAGAAGC
TTGAGCACTACCACCAGAAGCTCTGGGAGGTAGAACAGAATGGGGTGCTATGGCAGTGAAGAGATGTCTTCTGGGATGTG
CACCAAGGTCTGAAGGATGTGGGAGCAAAGGGACTGGCTTCAGTGAGGTTGTGGTGGACAGCGTCGAGGGTGGACTCTCC
AGTTTCTCCCAGGCCACCCCTTCAGCAGCAGGGGCTGTGGTCTCAAAACCCAGAGAGACCGCCTCAGTGATTCGGAATAA
ATTTGACAGTGCAGACAACATCTCTAATCTGAAAGACTACTTAGAGGAAGGGCTAGTGGAGGATGGGGGAAGATTTTGGG
GGTGATTTCAAACTTTCAAATGAGTCAAAATGTGGTAGTGAGGAAGATTGTTCAAGTGCCACATCAGGCTCAGTGGGAGC
CAACAGCATGACTGGGGCATTGCTGTAGGAGCATCCAGCTCCAAAACAAACACCGTGGACATGCAGAGCTCAGGATTTAA
TCCACATGAGATCCAGGAGATCTGGGAAACCCAGGCCAGGCTAGAGGAATCCTTTGGGACCCTCAAGGAACATTGTCAGA
GGGACTATTCCTTAATTATGCAGTTCTTACAGGAGGAGCAATGTAAGTGCGAATGATCAGAAGAACAACCAAATGACTTA
ACA

Alignment

ORF - retro_chof_1711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 75.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KQTESEQKLSKMTHNALENINVIGQG-LKHLFQHQRRRSSVSPHDVQQIQAEPEPEMDLESQNTCAEIDG
          ...ES.Q.L.K.......N.N..GQ..LK.LFQHQ..RSSVSPH..QQIQAE.EPEMD.ESQNT.AEID.
Retrocopy QRPESRQNLNKSCLQ*PTNVN--GQA<LKQLFQHQHSRSSVSPHGAQQIQAESEPEMDVESQNTGAEIDS

Parental  VSTHPTALNRVLQQIRVPPKMKRGTSLHSRRGKPEAPKGSPQINRRSGQEMAAVMQSGRPRSSSTTDAPS
          VSTHPTALNR.LQQI.VP.KMKRGTSLHSR.GKPEAPKGSPQ.NRRSGQEMAAVMQSGR.RSSSTTDAPS
Retrocopy VSTHPTALNRLLQQIQVPLKMKRGTSLHSRWGKPEAPKGSPQVNRRSGQEMAAVMQSGRLRSSSTTDAPS

Parental  SSAVIEIACAAAAAACLPGEEATAERIERLEVSSLAHTSSAVASSTDGSIHTDSVDGTPDPQRTKAAIAH
          .SAV.EIAC..AAAACLPG.EATAE....LE.SSLAHTSSAVASSTDGSIHTDS..GTPDPQ.TKAAIAH
Retrocopy GSAVMEIAC--AAAACLPG*EATAEQTKWLEASSLAHTSSAVASSTDGSIHTDSMSGTPDPQHTKAAIAH

Parental  LQQKILKLTEQIKIAQTARDDNVAEYLKLANSADKQQAARIKQVFEKKNQKSSQ-TILQLQKKLEHYHRK
          LQQKI.KL.EQI.IAQTARD.NV.EYLKLANSADKQ.AA.I.QVFEKKNQKSSQ.TILQLQKKLEHYH.K
Retrocopy LQQKIPKLPEQITIAQTARDNNVVEYLKLANSADKQPAACITQVFEKKNQKSSQ<TILQLQKKLEHYHQK

Parental  LREVEQNGIPRQPKDVFRDMHQGLKDVGA-KVTGFSEGVVDSVKGGLSSFSQATHSAAGAVVSKPREIAS
          L.EVEQNG...Q..DVF.D.HQGLKDVGA.K.TGFSE.VVDSV.GGLSSFSQAT.SAAGAVVSKPRE.AS
Retrocopy LWEVEQNGVLWQ*RDVFWDVHQGLKDVGA<KGTGFSEVVVDSVEGGLSSFSQATPSAAGAVVSKPRETAS

Parental  LIRNKFGSADNISNLKDSLEEGQVEDG-GKTLGVISNFQSS-PKYGSEEDCSSATSGSVGANSTTG-GIA
          .IRNKF.SADNISNLKD.LEEG.VEDG.GK.LGVISNFQ.S..K.GSEEDCSSATSGSVGANS.TG.GIA
Retrocopy VIRNKFDSADNISNLKDYLEEGLVEDG<GKILGVISNFQMS<SKCGSEEDCSSATSGSVGANSMTG<GIA

Parental  VGASSSKTNTLDMQSSGFDALLHEIQEIRETQARLEESFETLKEHYQRDYSLIMQTLQEERYRCERLEEQ
          VGASSSKTNT.DMQSSGF....HEIQEI.ETQARLEESF.TLKEH.QRDYSLIMQ.LQEE...CE..EEQ
Retrocopy VGASSSKTNTVDMQSSGFNP--HEIQEIWETQARLEESFGTLKEHCQRDYSLIMQFLQEEQCKCE*SEEQ

Parental  LNDLT
          .NDLT
Retrocopy PNDLT

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_1711 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,