RetrogeneDB ID: retro_chof_2237

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_60249:5594..6038(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNSTRN
• Ensembl ID: ENSCHOG00000007085
• Aliases: None
• Description: kinetochore-localized astrin/SPAG5 binding protein [Source:HGNC Symbol;Acc:30767]

Sequence

>retro_chof_2237
CAAACTCAAGCCATTTCTAAGTCTTGTTACCTGTTAAGTCCCAAGAAGTAGAAGTTTCCAAACTTCTTCATTCAAGAAGT
TCCGAGAGCAATGTTGAGAAAAACATCAAACCGAGACGAGAAAATGAGCAGACAAAAGCTGCAGACACTGCCATCAGAAG
GAACATTAGAAAATCTACAAACCATTGGGTAAGCAGAAATTGGAGGAACTCAAGGATAAGAACCAGCTTTCAGAGGCCAT
CAACAAGCAGTTGCACCTGCAGTTGACTGAAACTCAGGGAGGGCTGAAGGATCTGACCAGAAGGTGGAACTGCCAGGGAA
GTTTCAGGACAACAGCTTGGCACTCTTGGAGAGTAAGGGCATCAACCCAGTTTTAGGCAGCGAAACCCTTGCAGCACAAG
AATCCACTACGGATCACACGGACTCTATGTTGCTCCTGGAAACT

Alignment

ORF - retro_chof_2237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 70.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTQAISKS-LLPVKSKEVDVSKLLHSGSSENDVMKNIKPRRENGQTKTADTAIRKNIRKS-YKPLSKQKS
          QTQAISKS.LLPVKS.EV.VSKLLHS.SSE..V.KNIKPRREN.QTK.ADTAIR.NIRKS.YKPL.KQK.
Retrocopy QTQAISKS<LLPVKSQEVEVSKLLHSRSSESNVEKNIKPRRENEQTKAADTAIRRNIRKS<YKPLGKQKL

Parental  EEELKDKNQLLEAVNKQLHLKLTETQGELKNLT-QKVELLEKFQDNCLAILESKGISPVLGSETLASQQE
          .EELKDKNQL.EA.NKQLHL.LTETQG.LK.LT.QKVEL..KFQDN.LA.LESKGI.PVLGSETLA..QE
Retrocopy -EELKDKNQLSEAINKQLHLQLTETQGGLKDLT<QKVELPGKFQDNSLALLESKGINPVLGSETLAA-QE

Parental  STKDHTDSMLLLET
          ST.DHTDSMLLLET
Retrocopy STTDHTDSMLLLET

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_2237 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032340	2 retrocopies	retro_btau_1217, retro_btau_274,
Choloepus hoffmanni	ENSCHOG00000007085	3 retrocopies	retro_chof_1378, retro_chof_2237 , retro_chof_504,
Monodelphis domestica	ENSMODG00000000464	1 retrocopy	retro_mdom_1200,
Otolemur garnettii	ENSOGAG00000009825	1 retrocopy	retro_ogar_1829,
Tupaia belangeri	ENSTBEG00000012043	4 retrocopies	retro_tbel_2696, retro_tbel_3958, retro_tbel_4092, retro_tbel_787,
Tursiops truncatus	ENSTTRG00000010577	1 retrocopy	retro_ttru_240,