RetrogeneDB ID: retro_chof_1344

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_26854:5425..6216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNA12
• Ensembl ID: ENSCHOG00000003770
• Aliases: None
• Description: guanine nucleotide binding protein (G protein) alpha 12 [Source:HGNC Symbol;Acc:4380]

Sequence

>retro_chof_1344
GCGCTGCTCAAGTTCCGATACAGAATCGTCCGCAACATCCTCAAGGGCTTCAGAGACCTTCTTGATGCCAAGACAAGCTT
GGTATTCCTTGGCAGGATTCTGAAAATGAAAAGCATGGCATGTTCTTAAGGGCCTTTGAGATCAAAGCAGGGCTGCCAGT
GGAGCCGCCACCTTCCAGGTGTTGTACCTGCTTTGAGTGCTCTCTGGAGGTAATTGGTATCCAGGAAGTGTTCAGCCTGA
GAAGTGAGTTCTGGCTGGATGAATTACTGAAATACTTCTGGTTAACTTGGACCAGATTGGCCAGCTGAATTACTTTCCTT
ATAAGCAAGATATCCTGATATTTAGGAAAGCCACCAAGGGAATTGTAGAACATGATTTCATATCAAAAAAATCCCTTTTA
AGATGGTGGATGTGGGTGGCCAGCAGTCTCAGGGCCAGAAGTGGTTCCAGTGTTTTGAGAGGATCACATCCATCCTGCTC
ATGGTGTCCTCTAGTGAGTCGACTAGCGCCTCATGGAGGACAGGTGCACCAACCAGCTGGTGGAGTTGAAGAAAATCTTT
GAGAGCCTAGTCCACAACAAGCTCTTCTTCAAAGTCTCCATAATTCTGTTCCTCAACAAGATGGACTTTCTGGTGGAGAA
GGTGAAAATGGTCAGCATCAAGAAGCATTTCCCAGATTTCAAAAGTGACACCTATAGTCTAGAATATGTGCAGTGCTACT
TATTCCAGTGTTTTGACAGATACAGAATAAACCACAGTAAGCCACTCTTCCACCACTTCACCACTGCCATC

Alignment

ORF - retro_chof_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 70.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ALLEFRDTIV-NILKGSRVLVDAR-DKLGIPWQYSENEKHGMFLMAFENKAGLPVEP-ATFQLY-VPALS
          ALL.FR..IV.NILKG.R.L.DA..DKLGIPWQ.SENEKHGMFL.AFE.KAGLPVEP.ATFQ...VPALS
Retrocopy ALLKFRYRIVRNILKGFRDLLDAK<DKLGIPWQDSENEKHGMFLRAFEIKAGLPVEP<ATFQVL<VPALS

Parental  ALWR-DSGIREAFSRRSEFQLGESVKYF-LDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFV-IKKIP
          ALWR...GI.E.FS.RSEF.L.E..KYF.L.NLD.IGQLNYFP.KQDIL..RKATKGIVEHDF..IKKIP
Retrocopy ALWR<VIGIQEVFSLRSEFWLDELLKYF<LVNLDQIGQLNYFPYKQDILIFRKATKGIVEHDFI<IKKIP

Parental  FKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSE-YDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSI
          FKMVDVGGQ.SQ.QKWFQCF..ITSIL.MVSSSE..D..LMEDR.TN.LVE...IFE..V.NKLFF.VSI
Retrocopy FKMVDVGGQQSQGQKWFQCFERITSILLMVSSSE<VD*RLMEDRCTNQLVELKKIFESLVHNKLFFKVSI

Parental  ILFLNKMDLLVEKVKTVSIKKHFPDFRGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAI
          ILFLNKMD.LVEKVK.VSIKKHFPDF..D...LE.VQ.YL.QCFDR.R.N.SKPLFHHFTTAI
Retrocopy ILFLNKMDFLVEKVKMVSIKKHFPDFKSDTYSLEYVQCYLFQCFDRYRINHSKPLFHHFTTAI

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_1344 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003770	4 retrocopies	retro_chof_1344 , retro_chof_2083, retro_chof_601, retro_chof_653,
Choloepus hoffmanni	ENSCHOG00000012718	1 retrocopy	retro_chof_359,
Tursiops truncatus	ENSTTRG00000003798	1 retrocopy	retro_ttru_840,