RetrogeneDB ID: retro_chof_744

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_142498:3295..3895(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSCHOG00000013303
• Aliases: None
• Description: SPC25, NDC80 kinetochore complex component [Source:HGNC Symbol;Acc:24031]

Sequence

>retro_chof_744
ATGATAGAGGACAAACTGGCACTATTTGATAAAAGCATAAATGAATTTTGGAATAATTCAAAGGTACTGTCAGTGATACC
TCCTGTCAGATGGTGGGGCTAAGAGAGACCTACAAGGACTCCATTAAAGCATTTCAGAAAAGCTGTCTGTGATGTTAAAG
GAAGAAGACTGAATGGTTGAGATGTTGCTGGAATATCAAAATCAGATCTGCTGGCAGAATAAGTTCATTCAGGAAAAAAA
TGATAACTTGTTAAAGTTGATTGCTGAAGTAAAATGCAAAAAGCAAGAAATGGAAGTACTGACTGCAAATATCCAGGATC
TTAAGGAAGAATATGCAAAGAAGGAAACTATTTCCACTGCTAACAAAGCTAATGAAGAGAGAGGTTGAGAAAGCTGCAGA
AATATGCCGACTTATATAAAGACTGACTTGGACTAGAAATTTGAAAAATTTATGGTGATCAATTACAGTTTATATTCACT
AATATTGACCCTAAGCATCCTGTGAACCCATATATGTTTTCCTTGCACCTGAATGAAGCAAGGGACTATGAAGTGTCAGA
TAGTTCTCCATATCTCGAACACCTAGCAGATCTCAGAGAA

Alignment

ORF - retro_chof_744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 88.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIEDELALFDKSINEFWNK-FKSAVSDTSCQMVGLRDTYKDSIKAF-AEKLSMKLKEEDRMVEMFLEYQN
          MIED.LALFDKSINEFWN..FK..VSDTSCQMVGLR.TYKDSIKAF..EKLS..LKEED.MVEM.LEYQN
Retrocopy MIEDKLALFDKSINEFWNN<FKGTVSDTSCQMVGLRETYKDSIKAF<SEKLSVMLKEED*MVEMLLEYQN

Parental  QICQQNQRIQEKKDNLLKLIAEVKCKKQEMEVLTANIQDLKEEYAKKKETISTANKANE-ERLKRLQKSA
          QIC.QN..IQEK.DNLLKLIAEVKCKKQEMEVLTANIQDLKEEYAKK...........E.ERL..LQK.A
Retrocopy QICWQNKFIQEKNDNLLKLIAEVKCKKQEMEVLTANIQDLKEEYAKKETISTANKANEE<ERLRKLQKYA

Parental  DLYKDRLGLEIRKIYGDKLQFIFTNIDPKHPENPYMFSLRLNEARDYEVSDSAPYLEHLAEFQE
          DLYKD.LGLEI.KIYGD.LQFIFTNIDPKHP.NPYMFSL.LNEARDYEVSDS.PYLEHLA...E
Retrocopy DLYKD*LGLEI*KIYGDQLQFIFTNIDPKHPVNPYMFSLHLNEARDYEVSDSSPYLEHLADLRE

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_744 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541, retro_chof_2326, retro_chof_744 ,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,