RetrogeneDB ID: retro_chof_1543

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31989:9664..10808(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPT11
• Ensembl ID: ENSCHOG00000003906
• Aliases: None
• Description: septin 11 [Source:HGNC Symbol;Acc:25589]

Sequence

>retro_chof_1543
GAGGCAGGTATTGGCAAATCCACACTAATGGACACTTTATTCAACACCAAATTTGAAAGTGACCCGGCTTCTCACAATGA
ACCAGGTGTGCGGTTAAAAGCCAGAAGTTATGAACTTCAGGAGAGCAATGTATGGCTGAAGTTAACCATTGTTGACACCG
TGGGATTTGGAGACCAGATAAATAAAGATGACAGCTGTAAGCCAATAGTGGAGTACATTGATGCCCAATTTGAGGCCTAC
CTGCAAGAGGAATTGAAGATCAAATGTTCTCTCTTCAACTACCATGATGCAAGGATCCATGCCTGCCTCTACTTCATCGC
CCCTACCGGACATTCACTCAAGTCTCTGGACCTGGTCACCATGAAAAAGCTGGACAGTAAGGTGAACATCATTCCAATAA
TTGCAAAAGCTGATACCATTGCCAAGAATGAATTACACAAATTCAAGAGCAAGATCATGAGTGAACTAGTCAGCAATGGT
GTCCAGATATATCAGTTCCCCACAGATGAAGAAACGGTGGCAGAGATTAATGCAACAATGAGTGTCCATCTCCCATTTGC
AGTGGTTGGCAGCACAGAAGAGGTGAAGATCGGCAACAAGATGGCAAAAGCCAGGCAGTACCCCTGGGGGTGTGGTGCAG
GTTGAGAATGAAAACCATTGTGATTTTGTGAAACTCCGGGAGATGCTGATCCGAGTGAACATGGAAGATTTGCGGGAACA
GACTCACGCCCGCCACTATGAACTGTATCGGCACTGTAAGCTCGAGGAGATGGGCTTCAAAGACACTGATCCTGACAGCA
AGCCCTTCAGTCTTCAGGAAACATATGAAGCAAAGCGGAATGAATTCTTGGGAGAACTTCAGAAGAAAGAAGAAGAAATG
AGACAAATGTTTGTCATGAGAGTGAAAGAGAAAGAAGCTGAACTCAAAGAGGCAGAGAAAGAGCTTCATGAGAAGTTTGA
CCTCCTAAAGCGGACACACCAAGAAGAGAAGAAGAAAGTGGAAGACAAAAAGGAGGAGCTTGAGGAAGAGGTGAACAATT
TCCAGAAGAAGAAAGCAGCAGCTCAATTACTACAGTCCCAGGCCCAGCAGTCTAGGGCCCAGCAAACCAAGAAAGACAAG
GATAAGAAAAATGCAAGCTTCACA

Alignment

ORF - retro_chof_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 88.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETGIGKSTLMDTLFNTKFESDPASHNEPGVRLKARSYELQESNVRLKLTIVDTVGFGDQINKDDSYKPIV
          E.GIGKSTLMDTLFNTKFESDPASHNEPGVRLKARSYELQESNV.LKLTIVDTVGFGDQINKDDS.KPIV
Retrocopy EAGIGKSTLMDTLFNTKFESDPASHNEPGVRLKARSYELQESNVWLKLTIVDTVGFGDQINKDDSCKPIV

Parental  EYIDAQFEAYLQEELKIKRSLFNYHDTRIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTI
          EYIDAQFEAYLQEELKIK.SLFNYHD.RIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTI
Retrocopy EYIDAQFEAYLQEELKIKCSLFNYHDARIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTI

Parental  AKNELHKFKSKIMSELVSNGVQIYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWG
          AKNELHKFKSKIMSELVSNGVQIYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWG
Retrocopy AKNELHKFKSKIMSELVSNGVQIYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWG

Parental  -VVQVENENHCDFVKLREMLIRVNMEDLREQTHTRHYELYRRCKLEEMGFKDTDPDSKPFSLQETYEAKR
          .VVQVENENHCDFVKLREMLIRVNMEDLREQTH.RHYELYR.CKLEEMGFKDTDPDSKPFSLQETYEAKR
Retrocopy >VVQVENENHCDFVKLREMLIRVNMEDLREQTHARHYELYRHCKLEEMGFKDTDPDSKPFSLQETYEAKR

Parental  NEFLGELQKKEEEMRQMFVMRVKEKEAELKEAEKELHEKFDLLKRTHQEEKKKVEDKKKELEEEVNNFQK
          NEFLGEL....................ELKEAEKELHEKFDLLKRTHQEEKKKVEDKK.ELEEEVNNFQK
Retrocopy NEFLGELXXXXXXXXXXXXXXXXXXXXELKEAEKELHEKFDLLKRTHQEEKKKVEDKKEELEEEVNNFQK

Parental  KKAAAQLLQSQAQQSGAQQTKKDKDKKNASFT
          KKAAAQLLQSQAQQS.AQQTKKDKDKKNASFT
Retrocopy KKAAAQLLQSQAQQSRAQQTKKDKDKKNASFT

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_1543 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543 ,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Choloepus hoffmanni	ENSCHOG00000009949	1 retrocopy	retro_chof_2159,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Oryctolagus cuniculus	ENSOCUG00000001289	1 retrocopy	retro_ocun_1758,
Otolemur garnettii	ENSOGAG00000005210	1 retrocopy	retro_ogar_2831,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753,