RetrogeneDB ID: retro_cjac_4104

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:96640080..96641550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSCJAG00000014213
• Aliases: None
• Description: None

Sequence

>retro_cjac_4104
GGAAAGATGGCAGAGGTGTAGGGGGCCGAGGTGAAAGTGGATGGCACCAAGCTGAAACTGAGCTAGAATGAGCTGAAGAG
ATGCCTGAAAGCTGAGAAGAAAGTAGCAGAGAAGGAGGCCAAGCAGAAAGAGCTCAGTGAGAAACCCGATGCTGCCACCA
ACCACACGGCTGACAATGGTGTGGGTTCTGAGGAAGAGAGCCTGGACCCAAATCAATACTGCAAAATCCACAGTCAGGCA
ATTCATCAACTGAAGGTCAATGGGGAAGACCAATACCCACACAAGTTCCATATAGACATCTCACTCACCGACTTCATCGA
AGAATATAGTCACCACCTGCAGCCTGGGGATCACCTGACTGACATCACCTTAAGGGTGGCAGGTAGGATTCATGCCAAAA
GAGCTTCTGGGGTAAAGCTCATCTCCTATGATCTTCGAGGAGAGGGGTAAAGTTGCAAGTCATGGCCAATTCCAGAATTA
TAAATTGGAAAAATAATTTATTCATATTAATAACAAACTGCATCAGAGAGACATAATTGGAGTTGAGGGGAATCCTGGGA
AGACCAAGAAGGGTGAGCTGAGCATCATTCCATATGAGATCACACTGCTGTCTCCCTGTTTGCATATGTTACCTCATCTT
CACTTTGGCCTCAAAGAAAAGGAAACAAGGTATCGCCAGAGATACTTGGACTTGATCCTGAATGACTTTGTGAGGCAGAA
ATTTATCACCCGCTCTAAGATCATCACATATATAAGAAGTTTCATGGATGAGCTGGGATTCCTGGGACCGAAACTCCCAT
TATGAACATCATCCCAGGGGGAGCTGTGGCCAAGCCTTTCATCACTTAGCACAATGAGCTGGACATGAATTTTTATGTGA
GAATTGCTCCAGAACTCTACCATGAGATGCTTGTGGTTGGTGGCATCGACCGGGTTTTTGAAATTGGATGCCAGTTCCGG
AATGAGGGGATTGATTTGATGCACAATCCTGAGTTCACCACCTGTGAGTTCTACATGGCCTATGCAGACTATCACAATCT
CATAGAAGTCATGGAGAACATGGTTTCAGTGATGGTGAAGCATGTTACGGGCGGTTACAAGGTCATCTACCACCCAGATG
GCCCAGAGGGCCAGGCCTATGATATTCACTTCACCCCACCCTTTCGGAGAATCAGCATGGTAGAAGAGCTTGAGAAAGCC
TTGAGGATGAAGCTACTAGAAACTAACCTCTTTGAAACTGAAGAAACTTGCAAAATTCTTGATGATATCTGGGGGGCAAA
AGCTGTTGAATGCCCTCCACCTCGGACCACAGCCAGGCTCCTTGACAAGCTTGTAGGGGAGTTACTGGAAATGACTTGCA
TCAATCCTACGTTCATTTTTGATCACCCACAGATAATGAGCCCTTTGGCTAAATGGCACTGCTCTAAAGAGGGTCTGACC
GAGAGCTTTGAGCTATTTGTCATGAAGAGA

Alignment

ORF - retro_cjac_4104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.39 %
• Parental protein coverage: 81.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAEVQVDGTEPKLSKNELKRRLKAEKKV--AEKEAKQKELSEKQLSQATAAATNHTADNGVGPEEESLDP
          G....V.G.E.K.....LK......K....AEK....KE...K.LS....AATNHTADNGVG.EEESLDP
Retrocopy GKMAEV*GAEVKVDGTKLKLS*NELKRCLKAEKKVAEKEAKQKELSEKPDAATNHTADNGVGSEEESLDP

Parental  NQYYKIRSQAIHQLKVSGEDPYPHKFHVDISLTDFIQEYSH-LQPGDHLTDITLRVAGRIHAKRASGGKL
          NQY.KI.SQAIHQLKV.GED.YPHKFH.DISLTDFI.EYSH.LQPGDHLTDITLRVAGRIHAKRASG.KL
Retrocopy NQYCKIHSQAIHQLKVNGEDQYPHKFHIDISLTDFIEEYSHHLQPGDHLTDITLRVAGRIHAKRASGVKL

Parental  IFYDLRGEG-VKLQVMANSR-NYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCL
          I.YDLRGEG.VKLQVMANSR.NYK.E..FIHINNKL...DIIGV.GNPGKTKKGELSIIPYEITLLSPCL
Retrocopy ISYDLRGEG<VKLQVMANSR<NYKLEK*FIHINNKLHQRDIIGVEGNPGKTKKGELSIIPYEITLLSPCL

Parental  HMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFLE-IETPMMNIIPGGAV
          HMLPHLHFGLK.KETRYRQRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFL...ETP.MNIIPGGAV
Retrocopy HMLPHLHFGLKEKETRYRQRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFLG<TETPIMNIIPGGAV

Parental  AKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHD
          AKPFIT.HNELDMN.Y.RIAPELYH.MLVVGGIDRV.EIG.QFRNEGIDL.HNPEFTTCEFYMAYADYH.
Retrocopy AKPFIT*HNELDMNFYVRIAPELYHEMLVVGGIDRVFEIGCQFRNEGIDLMHNPEFTTCEFYMAYADYHN

Parental  LMEITEKMVSGMVKHITGGYKVTYHPDGPEGQAYEIDFTPPFRRISMIEELEKALGMKLPETNLFETEET
          L.E..E.MVS.MVKH.TGGYKV.YHPDGPEGQAY.I.FTPPFRRISM.EELEKAL.MKL.ETNLFETEET
Retrocopy LIEVMENMVSVMVKHVTGGYKVIYHPDGPEGQAYDIHFTPPFRRISMVEELEKALRMKLLETNLFETEET

Parental  RKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELF
          .KILDDI..AKAVECPPPRTTARLLDKLVGE.LE.TCINPTFI.DHPQIMSPLAKWH.SKEGLTE.FELF
Retrocopy CKILDDIWGAKAVECPPPRTTARLLDKLVGELLEMTCINPTFIFDHPQIMSPLAKWHCSKEGLTESFELF

Parental  VMKK
          VMK.
Retrocopy VMKR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	29.71 RPM
SRP051959_heart	0.07 RPM	37.71 RPM
SRP051959_kidney	0.04 RPM	35.70 RPM
SRP051959_liver	0.04 RPM	42.04 RPM
SRP051959_lung	0.02 RPM	32.99 RPM
SRP051959_lymph_node	0.07 RPM	35.57 RPM
SRP051959_skeletal_muscle	0.11 RPM	93.95 RPM
SRP051959_spleen	0.00 RPM	32.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4104 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4104 has 0 orthologous retrocopies within eutheria group .

---

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,