RetrogeneDB ID: retro_chof_167

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3792:14378..15816(-)
• Located in intron of: ENSCHOG00000013258

Retrocopy information

• Ensembl ID: ENSCHOG00000013279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013540
• Aliases: None
• Description: None

Sequence

>retro_chof_167
AGAGTAGTTATTTTGATGGAACTAGAAGTTTTGAAATCAGCTGAAGCAGTTGGATTAAAGATTGGCAATCCAGTACCCTA
TAATGAAGGACATGGGCAGCAGCAGGTTGTTCCTACTCCTGTGTCAGCAACCAGTCCACCAACCAGCAAGCCCCAGCAAC
AGAATGGAAGTTCAGGAATGGGTTCCACCGTATCTAAGTCTTTTGGTGTCTCAAAGACATTTGGAAAAGCTGGAAATACT
AACCTCATGAACAGTCCCGGGGGGAACACAGTCCAAAGTGGTACCCATTGCCAGCCTTACCCCTTACCAGTCCAAGTGGA
CTATTTGTGCTCGAGTTACCAATAAAAGTCAGATCCGTACCTGGAGCAATTCCCGAGGGGAAGGAAAGCTTTTCTCTTTA
GAACTGGTTGATGAAAGTGGTGAAATCAGAGTTACTGCTTTCAACGAGCAAGTGGACAAGTTCTTTCCCCTTATTGAAGT
GAACAAGGTTTATTATTTCTCAAAAGGCACCCTAAAGATTGCTAACAAGCAATTCACAGCTGTTAAAAATGACTATGAGA
TGACCTTCAATAATGAGACATCTGTCATGCCCTGTGAAGATGGTCATCATTTACCTACAGTTCACTTTGATTTCACTGGG
ATTGGTGAACTAGAGAATAAGTCTAAAGACTCACTTGTAGACATAATTGGAATCTGCAAGAATTATGAAGATGCCACTAA
AATCACAGTGAAATCTAATAACAGAGAAGTTTCTAAGAGAGATATCTACCTGATGGACATGTCAGGGAAGGTGGTGACTG
CTACTCTGTGGGGAGAAGATGCTGATAGATTTGATAGTTCTAGACAGCCCATGATGGCTATCAAAGGAGCCAGAGTTTCT
GATTTTGGTGGACGGAGCCTCTCTGTACTGTCTTCAAGCACTGTCATTGTGAATCCTGACATCCCAGAGGCCTATAAGCT
TCGTGGATGGTTTGACTCAGAAGGACAAGCCTTAGATGGTGTTTCCATCTCTGATCTAAAGAGTGGAGGAGTAGGAGGGG
GCAACACCAACTGGAAAACCCTGTATGAGGTTAAATCAGAGAATCTGGGTCAAGGTGACAAGGCGGACTATTTCAGCTGT
GTGGCAACAGTGGTGTATCTCCGCAAGGAGAATTGTATGTACCAGGCCTGCCCAACTCAGGACTGCAACAAGAAAGTGAT
TGATCAGCAGAATGGATTATACCGCTGTGAGAAGTGTGACAGTGAATTTCCCAATTTCAAGTACCGCATGATCCTATCAG
TAAATATTGCAGATTTTCAAGAGAATCAGTGGGTGACTTCTTTCCAGGAGTCTGCAGAGGCTATCCTCGGACAAAGTGCT
GCTTATCTGGGGGAATTAAAAGAGAAGAATGAGCAGGCATTTGAGGAAGTTTTCCAGAACGCCAACTTTCGATCTTTC

Alignment

ORF - retro_chof_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 81.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVVILMELEVLKSAEAVGLKIGNPVPYNEGHGQQQVVPTPVSATSPPTSKPQQQNGSSGMGSTVSKSFGV
          RVVILMELEVLKSAEAVGLKIGNPVPYNEGHGQQQVVPTPVSATSPPTSKPQQQNGSSGMGSTVSKSFGV
Retrocopy RVVILMELEVLKSAEAVGLKIGNPVPYNEGHGQQQVVPTPVSATSPPTSKPQQQNGSSGMGSTVSKSFGV

Parental  SKTFGKAGNTNLMNSPGG-TQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES
          SKTFGKAGNTNLMNSPGG.TQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES
Retrocopy SKTFGKAGNTNLMNSPGG>TQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES

Parental  GEIRVTAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDGHHLPTVHF
          GEIRVTAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDGHHLPTVHF
Retrocopy GEIRVTAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDGHHLPTVHF

Parental  DFTGIGELENKSKDSLVDIIGICKNYEDATKITVKSNNREVSKRDIYLMDMSGKVVTATLWGEDADRFDG
          DFTGIGELENKSKDSLVDIIGICKNYEDATKITVKSNNREVSKRDIYLMDMSGKVVTATLWGEDADRFD.
Retrocopy DFTGIGELENKSKDSLVDIIGICKNYEDATKITVKSNNREVSKRDIYLMDMSGKVVTATLWGEDADRFDS

Parental  SRQPVMAIKGARVSDFGGRSLSVLSSSTVIVNPDIPEAYKLRGWFDSEGQALDGVSISDLKSGGVGGGNT
          SRQP.MAIKGARVSDFGGRSLSVLSSSTVIVNPDIPEAYKLRGWFDSEGQALDGVSISDLKSGGVGGGNT
Retrocopy SRQPMMAIKGARVSDFGGRSLSVLSSSTVIVNPDIPEAYKLRGWFDSEGQALDGVSISDLKSGGVGGGNT

Parental  NWKTLYEVKSENLGQGDKADYFSCVATVVYLRKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNF
          NWKTLYEVKSENLGQGDKADYFSCVATVVYLRKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNF
Retrocopy NWKTLYEVKSENLGQGDKADYFSCVATVVYLRKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNF

Parental  KYRMILSVNIADFQENQWVTSFQESAEAILGQSAAYLGELKEKNEQAFEEVFQNANFRSF
          KYRMILSVNIADFQENQWVTSFQESAEAILGQSAAYLGELKEKNEQAFEEVFQNANFRSF
Retrocopy KYRMILSVNIADFQENQWVTSFQESAEAILGQSAAYLGELKEKNEQAFEEVFQNANFRSF

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_167 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013540	2 retrocopies	retro_chof_167 , retro_chof_2578,
Rattus norvegicus	ENSRNOG00000003123	1 retrocopy	retro_rnor_1373,
Ictidomys tridecemlineatus	ENSSTOG00000022475	1 retrocopy	retro_itri_677,