RetrogeneDB ID: retro_chof_2324

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6600:21829..23231(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSCHOG00000013447
• Aliases: None
• Description: lysyl-tRNA synthetase [Source:HGNC Symbol;Acc:6215]

Sequence

>retro_chof_2324
AGGATCCATGCCAAAAGAGCTTCTGGGGGAAAGCTCATCTTCTATGACCTTCGAGGAGAGGGTGTCAAGTTGCAAGTCAT
GGCCAATTGCAGGAATTATAAATCAGAAGAAGAATTTATTAAAATCAATAATAAGCTGCATAGGGGAGACATAATTGGAG
TTCAGGGGAATCCTGGGAAAACCAAGAAGGGTGAGCTGAGCATCATTCCCTATGAGATCACGTTACTGTCTTCTTGCTTG
CACATGCTACCTCATCTTCACTTTGGCCTCAAAGACAAGGAAACATGATATCGTCAGAGATACCTGGACTTGATCCTGAA
TGACTTTGTGAGGCAGAAATTTATCATCCATTCTAAGATCATCACATATATAAGAAGTTTCTTGGATGAGTTGGGATTCT
TAGAGATTGAAACTCCCATGATGAACATTATACCAGGGGGAGCTGTGGCCAAGCCTTTCATCACCTACCACAATGAGCTG
GACATGAACTTATATATGAGAATTGCTCCAGAACTCTACCATAAGATGCTGGTTGTTGGAGGCATTGACTGGGTATATGA
GATTGGACGCCAGTTCCGGAATGAAGGAATTGATTTAACTCACAATCCTGAGTTCACTACCTGTGAGTTCTACATGGCCT
ACGCAGACTATCATGATCTCATGGAAATCACAGAGAAGATGATTTCAGGAATGGTAAAGCACATTACAGGCAGTTACAAG
GTCACCTACCATCCAGATGGCCCAGAGGGCCAAGCCTACGAGATTGACTTCACCCCCACCATTCCGGAGAATCAACATGG
TAGAAGAACTCAAGAAAGCTCTGGGGGTGAAACTGCCAGAAACTAATCTCTTCGAAACTGAGGAAACTCGCAAAATTCTT
GATGATATCTGTGTGGCAAAGGCTGTTGAATGCACTCTACCTCGGACCACAGCCAGGCTTCTTGATAAGCTTGTTGGAGA
GTTCCTGGAAGTGACTTGCATTGATCCTACATTCATCAGTGATCACCCGCAGATAATGAGCCCTTTGGCCAAGTGGCATC
GCTCCAAAGAGGGTCTAATGGAGCACTTTGAGCTGTTTGTCATGAAGAAGGAAATCTGCAATGCCTACACTGAGCTGAAT
GACCCCATGCAGCAGCAGCAACTTTTTGAAGAACAAGCCAAGGCCAAGGCTGCTGGTGATGATGAGGCCATGTACATAGA
TGAAAACTTCTGTACCGCTCTGGAATACGGGCTGCCCCCAACAGCTGGCTGGGGCATGGGCATTGACCGTGTTACTATGT
TCCTCACAGACTCCAATAACATCAAGGAAGTACTTCTGTTTCCTGCCATGAAACCTGAAGACAAGAAGGAGAATGTAGCA
ACCACTGATACATTGGAAAGCACAACAGTTGGCACATCAGTC

Alignment

ORF - retro_chof_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 74.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIHAKRASGGKLIFYDLRGEGVKLQVMANCRNYKSEEEFIKINNKLHRGDIIGVRGNPGKTKKGELSIIP
          RIHAKRASGGKLIFYDLRGEGVKLQVMANCRNYKSEEEFIKINNKLHRGDIIGV.GNPGKTKKGELSIIP
Retrocopy RIHAKRASGGKLIFYDLRGEGVKLQVMANCRNYKSEEEFIKINNKLHRGDIIGVQGNPGKTKKGELSIIP

Parental  YEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPM
          YEITLLS.CLHMLPHLHFGLKDKE...................FII.SKIITYIRSFLDELGFLEIETPM
Retrocopy YEITLLSSCLHMLPHLHFGLKDKEXXXXXXXXXXXXXXXXXXXFIIHSKIITYIRSFLDELGFLEIETPM

Parental  MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEF
          MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGID.VYEIGRQFRNEGIDLTHNPEFTTCEF
Retrocopy MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDWVYEIGRQFRNEGIDLTHNPEFTTCEF

Parental  YMAYADYHDLMEITEKMISGMVKHITGSYKVTYHPDGPEGQAYEIDFTP-PFRRINMVEELEKALGVKLP
          YMAYADYHDLMEITEKMISGMVKHITGSYKVTYHPDGPEGQAYEIDFTP.PFRRINMVEEL.KALGVKLP
Retrocopy YMAYADYHDLMEITEKMISGMVKHITGSYKVTYHPDGPEGQAYEIDFTP>PFRRINMVEELKKALGVKLP

Parental  ETNLFKTEETRKILDDICVAKAVECTPPRTTARLLDKLVGEFLEVTCIDPTFICDHPQIMSPLAKWHRSK
          ETNLF.TEETRKILDDICVAKAVECT.PRTTARLLDKLVGEFLEVTCIDPTFI.DHPQIMSPLAKWHRSK
Retrocopy ETNLFETEETRKILDDICVAKAVECTLPRTTARLLDKLVGEFLEVTCIDPTFISDHPQIMSPLAKWHRSK

Parental  EGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMYIDENFCTALEYGLPPTAGWGM
          EGL.E.FELFVMKKEICNAYTELNDPM.Q.QLFEEQAKAKAAGDDEAMYIDENFCTALEYGLPPTAGWGM
Retrocopy EGLMEHFELFVMKKEICNAYTELNDPMQQQQLFEEQAKAKAAGDDEAMYIDENFCTALEYGLPPTAGWGM

Parental  GIDRVTMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV
          GIDRVTMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV
Retrocopy GIDRVTMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV

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_2324 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013447	1 retrocopy	retro_chof_2324 ,
Callithrix jacchus	ENSCJAG00000014213	2 retrocopies	retro_cjac_4104, retro_cjac_608,
Homo sapiens	ENSG00000065427	1 retrocopy	retro_hsap_1191,
Gorilla gorilla	ENSGGOG00000005515	1 retrocopy	retro_ggor_930,
Mus musculus	ENSMUSG00000031948	8 retrocopies	retro_mmus_3536, retro_mmus_3537, retro_mmus_3538, retro_mmus_3539, retro_mmus_3540, retro_mmus_3541, retro_mmus_3542, retro_mmus_3543,
Nomascus leucogenys	ENSNLEG00000013072	1 retrocopy	retro_nleu_2080,
Pongo abelii	ENSPPYG00000007567	1 retrocopy	retro_pabe_992,
Pan troglodytes	ENSPTRG00000008364	1 retrocopy	retro_ptro_3036,
Pteropus vampyrus	ENSPVAG00000006746	2 retrocopies	retro_pvam_1301, retro_pvam_723,
Sorex araneus	ENSSARG00000011493	1 retrocopy	retro_sara_415,