RetrogeneDB ID: retro_chof_702

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_137087:668..1791(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS36
• Ensembl ID: ENSCHOG00000008949
• Aliases: None
• Description: vacuolar protein sorting 36 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20312]

Sequence

>retro_chof_702
ATCACCGAGACCCTGGTGATCCAGCAGCGCAGGGTACACATCTACGACGGCGAGGAGAAGATAAAATTTGATGCTGGGGC
CCTCCTTCTCAGTACACACCAACTAATTTGGAGAGATCTGAAAAACCATGAATGCTGCATGGCCATTCCTCTTTCCCAAA
TTGTGTTCATTGAAGAACAGGCAGCTGGCATTGGGAAAAGTGCCAAAATAGTGGTTCATCTTCACCCAGCACCTCCTAAC
AAAGGACCTGGGCCATTCCAAAGTAGTAAGAATTCCTATATCAAGCTCTCCTTCAAAGAACATGGCCAGATTGAGTTCTA
CAGGCGTTTTATCAGAGGAAATGACACAGAGAAGATGAGAGAATATGCCAGTTTCCCAGTCCGTACAAACAAGTAGAGGA
CACCAGCCAGGAAGAATAAGGGCTGTAGAAATTGTAGGTATTGAAAGGAAACAGGAAGAAAAAAGAAAAGAAGCTGACAA
AAATATTTCTGAGGCCTTTGAGGACCTCAGCAAGCTAATGATCAAGGCTAAGGAAATGGTGGAGTTATCAAAATCAATTG
CTAATAAAATTAAAGACAAACAAGGTGACATCACAGAAGATGAGACTATCAGGTTTAACTCCTACTTGCTAAGCATGGGA
ATAGCTAACCCAGTTACCAGGGAAACCTACAGCTCAGGCACACAGTACCACATGCAGCTGGCCAAACAGCTGGTTGGAAT
ACTACAGGCACCTTTAGAGGAATGAGGAGAAATAATGTCTCTGACGGAGGTGTACTGTTTAGTAAACTGTGCTCAAGGAA
TGGAATTGCTCTCACCAGAAGATTTAGTGAATGCATGAAAGATGCTAGAAGCACTGAAATTACCTCTCAGGCTCCGAGTT
TTTGACAGTGGTGTCATGGTACTTGAGTGTCAGTCCCACAGGGAGGAGGAAATGGTGGCCTTGGCCCTACAGACAGTTTC
AGAGAAGAGATCATTAACATCAGAAGAGTTTGCCAAGCTTGTGGGAATGTCCGTCCTCCTGGCCAAAGAACGGTTGCTTC
TTGCAGAGAAGATGGGCCATCTTTGCCGAGATGACTCAGTGGAAGGCTTGCGGTTTTATCCAAATCTATTTATGACACAG
AGC

Alignment

ORF - retro_chof_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.8 %
• Parental protein coverage: 97.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTETLVIHQHRAHIFNFKEKIKFDAGALLLSTHRLIWRDLKNHECCMAIPLSQIVFIEEQAAGIGKSAKI
          .TETLVI.Q.R.HI....EKIKFDAGALLLSTH.LIWRDLKNHECCMAIPLSQIVFIEEQAAGIGKSAKI
Retrocopy ITETLVIQQRRVHIYDGEEKIKFDAGALLLSTHQLIWRDLKNHECCMAIPLSQIVFIEEQAAGIGKSAKI

Parental  VVHLHPAPPNKEPGPFQSSKNSYIKLSFKEHGQIEFYRR-LSEEMTQRRWENMPVSQSVQTSRGHQPGRI
          VVHLHPAPPNK.PGPFQSSKNSYIKLSFKEHGQIEFYRR.LSEEMTQRR.ENMPVSQSVQTSRGHQPGRI
Retrocopy VVHLHPAPPNKGPGPFQSSKNSYIKLSFKEHGQIEFYRR>LSEEMTQRR*ENMPVSQSVQTSRGHQPGRI

Parental  RAVGIVGIERKLEEKRKETDKNISEAFEDLSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYL
          RAV.IVGIERK.EEKRKE.DKNISEAFEDLSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRF.SYL
Retrocopy RAVEIVGIERKQEEKRKEADKNISEAFEDLSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFNSYL

Parental  LSMGIANPVTRETYGSGTQYHMQLAKQLVGILQAPLEERGGIMSLTEVYCLVNRARGMELLSPEDLVNAC
          LSMGIANPVTRETY.SGTQYHMQLAKQLVGILQAPLEE.G.IMSLTEVYCLVN.A.GMELLSPEDLVNA.
Retrocopy LSMGIANPVTRETYSSGTQYHMQLAKQLVGILQAPLEE*GEIMSLTEVYCLVNCAQGMELLSPEDLVNA*

Parental  KMLEALKLPLRLRVFDSGVMVLELQSHKEEEMVASALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAE
          KMLEALKLPLRLRVFDSGVMVLE.QSH.EEEMVA.AL.TVSEK.SLTSEEFAKLVGMSVLLAKERLLLAE
Retrocopy KMLEALKLPLRLRVFDSGVMVLECQSHREEEMVALALQTVSEKRSLTSEEFAKLVGMSVLLAKERLLLAE

Parental  KMGHLCRDDSVEGLRFYPNLFMTQS
          KMGHLCRDDSVEGLRFYPNLFMTQS
Retrocopy KMGHLCRDDSVEGLRFYPNLFMTQS

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_702 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008949	1 retrocopy	retro_chof_702 ,
Macaca mulatta	ENSMMUG00000011360	1 retrocopy	retro_mmul_2510,
Otolemur garnettii	ENSOGAG00000011312	1 retrocopy	retro_ogar_913,
Ictidomys tridecemlineatus	ENSSTOG00000004651	1 retrocopy	retro_itri_97,