RetrogeneDB ID: retro_chof_1378

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_27677:3530..4173(-)
• 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_1378
ACAGAAATGGGAGCCATTTCTCTGAGCCTATTACCTGTTAACTCCAAAGAAGTAGACATTTCCAAACAACATCACTCAGA
AAGTTCAGAGTGTAATGTTATGAGAATCATCCAACCAAGATGAGAGAATGGACAGAGGAAAGTTGCAGACACCGCCACTG
GAAAGAATGTTAGAAAGAGCTACAAGCCATTGAGCAAGCAGATCAGAGGAAGAACTCAAGAATAAGAACCAACTCTTAGA
GTCAGTCAAGAAGCCATTGCACCTGAAGTTGACTGAAACTCAGGGAGAGCTGAAGGACCTGATGTAGAAGGTGGAGCTGC
TGGAGAAGTTTCAGGATAACTGTTTGGCAGTTTTGGAGAGCATGGGCATTGATCTAGTTTTAGACAAGGAGATCTTGGTA
TCACAACAAGAATCCACTATGGATCCCATGCAGTATATGTTGCTGTTGGAAGCTTTGCAAGATGAGCTGAAACTTCTTAA
TGAAACAGCCAAAAATTATTCAGAGGAGTTACAGGAGTTACAAAATATAGTTGAAGATGTAAGATGAAGAAAGGATCAGT
TCCTAGAACAGCAAACCATATTAACACATCAAGTAAGTGATTCGACAACAGCCCTTGAGGAAATGGAGCAGTTATTAGAA
ATA

Alignment

ORF - retro_chof_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TQTQAISKSLLPVKSKEVDVSKLLHSGSSENDVMKNIKPRRENGQTKTADTAIRKNIRKSYKPLSKQ-KS
          T...AIS.SLLPV.SKEVD.SK..HS.SSE..VM..I.PR.ENGQ.K.ADTA..KN.RKSYKPLSKQ...
Retrocopy TEMGAISLSLLPVNSKEVDISKQHHSESSECNVMRIIQPR*ENGQRKVADTATGKNVRKSYKPLSKQ>SE

Parental  EEELKDKNQLLEAVNKQLHLKLTETQGELKNLTQKVELLEKFQDNCLAILESKGISPVLGSETLASQQES
          EE.LK.KNQLLE.V.K.LHLKLTETQGELK.L..KVELLEKFQDNCLA.LES.GI..VL..E.L.SQQES
Retrocopy EE-LKNKNQLLESVKKPLHLKLTETQGELKDLM*KVELLEKFQDNCLAVLESMGIDLVLDKEILVSQQES

Parental  TKDHTDSMLLLETLQDELQLFNETAKKQMEELQAL-KVKLKLKDEERI-RFLEQQTVCNSQVNDFTTALE
          T.D....MLLLE.LQDEL.L.NETAK...EELQ.L.K..LK..DEERI..FLEQQT....QV.D.TTALE
Retrocopy TMDPMQYMLLLEALQDELKLLNETAKNYSEELQEL>KI*LKM*DEERI<QFLEQQTILTHQVSDSTTALE

Parental  EMEKLLEM
          EME.LLE.
Retrocopy EMEQLLEI

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_1378 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,