RetrogeneDB ID: retro_cjac_608

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:123096858..123098647(-)
• 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_608
ATGGCAGCAGTGCACAGGGCTGAGGTGCAAGTGGATGGCACCGAGCCGAAACTGAACAAGAATGAGCTGAAGAGACGCCT
GAAAGCTGAGAAGAAAGTAGCAGAGAAGGAGGCCAAGCAGAAAGAGCTTAGTGAGAAACAGCTAAGCCAAGCCACCGCTG
CTGCCACCAACCACACTGCTGACAATGGTGTGGGTCCTGAGGAAGAGAGCCTGGACCCAAATCAATACTACAAAATCCGC
AGTCAAGCAATTCATCAGCTGAAGGTCAGTGGGGAAGACCCATACCCACACAAGTTCCATGTAGACATCTCACTCACCGA
CTTCATCCAAGAATATAGTCACCTGCAGCCTGGGGATCACCTGACTGACATCACCTTAAGGGTGGCAGGTAGGATTCATG
CCAAAAGAGCTTCTGGGGGAAAGCTTATCTTCTATGATCTTCGAGGAGAGGGGGTGAAGTTGCAAGTCATGGCCAATTCC
AGAAATTATAAATCAGAAGAAGAATTTATTCATATTAATAACAAACTGCGTCGGGGAGACATAATTGGAGTTCAGGGGAA
TCCTGGGAAGACCAAGAAGGGTGAACTGAGCATCATTCTGTATGAGATCACACTGCTGTCTCCCTGTTTGCATATGTTAC
CTCATCTTCACTTTGGCCTCAAAGACAAGGAAACAAGGTATCACCAGAGATACCTGGACTTGATCCTGAATGACTTCGTG
AGGCAGAAATTTATCACCCGCTCTAAGATCATCACATATATAAGAAGTTTCATGGATGAGCTGGGATTCCTGGAGATTGA
AACTCCCATGATGAACATCATCCCAGGGGGAGCTGTGGCCAAGCCTTTCATCACTTATCACAATGAGCTGGACATGAACT
TATATATGAGAATTGCTCCAGAACTCTACCATGAGATGCTTGTGGTTGGTGGCATCGATCGGGTTTATGAAATTGGACGC
CAGTTCCGGAATGAGGGGATTGATTTGACACACAATCCTGAGTTCACCACCTGTGAGTTCTACATGGCCTATGCAGACTA
TCACGATCTCATGGAAATCACGGAGAAAATGGTTTCAGGGATGGTGAAGCATATTACAGGTGGTTATAAAGTCACCTACC
ACCCAGATGGCCCAGAGGGCCAGGCCTATGAAATTGACTTCACCCCACCCTTCCGGAGAATCAGCATGATAGAAGAGCTT
GAGAAATCCCTGGGGATGAAGCTGCCAGAAACTAACCTCTTTGAAACTGAAGAAACTCGCAAAATTCTTGATGATATCTG
TGTGGCAAAAGCTGTCGAATGCCCTCCACCTCGGACCACAGCCAGGCTCCTTGACAAGCTTGTAGGGGAGTTCCTGAGGG
TAACTTTGCATCAATCCTACGTTCATCTGTGATCACCCACAGATAATGAGCCCTTTGGCTAAATGGCACCGCTCTAAAGA
GGGTCTGACAGAGCGCTTTGAGCTATTTGTCATGAAGAAAGAGATATGTAATGCCTACACTGAGCTGAATGATCCCATGC
GGTAGCGGCAGCTTTTTGAAGAACGGGCCAAGGCCAAGGCTGCAGGTGATGATGAGGCCATGTTCATAGATGAAAACTTC
TGTACCACCCTGGAATACGGGCTGCCCCCCACGGCTGGCTGGGGCATGGGCATTGACCGAGTCGCCATGTTTCTCACGGA
CTCCAACAACATCAAGGAAGTACTTCTGTTTCCTGCCATGAAACCTGAAGACAAGAAGGAGAATGTAGCACCCACTGAGA
CGCTGGAAAGTACAGTTGGCACTTCTGTC

Alignment

ORF - retro_cjac_608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVHGAEVQVDGTEPKLSKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTADNGVGPEEES
          MAAVH.AEVQVDGTEPKL.KNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTADNGVGPEEES
Retrocopy MAAVHRAEVQVDGTEPKLNKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTADNGVGPEEES

Parental  LDPNQYYKIRSQAIHQLKVSGEDPYPHKFHVDISLTDFIQEYSHLQPGDHLTDITLRVAGRIHAKRASGG
          LDPNQYYKIRSQAIHQLKVSGEDPYPHKFHVDISLTDFIQEYSHLQPGDHLTDITLRVAGRIHAKRASGG
Retrocopy LDPNQYYKIRSQAIHQLKVSGEDPYPHKFHVDISLTDFIQEYSHLQPGDHLTDITLRVAGRIHAKRASGG

Parental  KLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCL
          KLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSII.YEITLLSPCL
Retrocopy KLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIILYEITLLSPCL

Parental  HMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFLEIETPMMNIIPGGAVA
          HMLPHLHFGLKDKETRY.QRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFLEIETPMMNIIPGGAVA
Retrocopy HMLPHLHFGLKDKETRYHQRYLDLILNDFVRQKFITRSKIITYIRSFMDELGFLEIETPMMNIIPGGAVA

Parental  KPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDL
          KPFITYHNELDMNLYMRIAPELYH.MLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDL
Retrocopy KPFITYHNELDMNLYMRIAPELYHEMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDL

Parental  MEITEKMVSGMVKHITGGYKVTYHPDGPEGQAYEIDFTPPFRRISMIEELEKALGMKLPETNLFETEETR
          MEITEKMVSGMVKHITGGYKVTYHPDGPEGQAYEIDFTPPFRRISMIEELEK.LGMKLPETNLFETEETR
Retrocopy MEITEKMVSGMVKHITGGYKVTYHPDGPEGQAYEIDFTPPFRRISMIEELEKSLGMKLPETNLFETEETR

Parental  KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVT-CINPTFICDHPQIMSPLAKWHRSKEGLTERFELF
          KILDDICVAKAVECPPPRTTARLLDKLVGEFL.VT.CINPTFICDHPQIMSPLAKWHRSKEGLTERFELF
Retrocopy KILDDICVAKAVECPPPRTTARLLDKLVGEFLRVT>CINPTFICDHPQIMSPLAKWHRSKEGLTERFELF

Parental  VMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLT
          VMKKEICNAYTELNDPMR.RQLFEE.AKAKAAGDDEAMFIDENFCT.LEYGLPPTAGWGMGIDRVAMFLT
Retrocopy VMKKEICNAYTELNDPMR*RQLFEERAKAKAAGDDEAMFIDENFCTTLEYGLPPTAGWGMGIDRVAMFLT

Parental  DSNNIKEVLLFPAMKPEDKKENVAPTETLESTAVGTSV
          DSNNIKEVLLFPAMKPEDKKENVAPTETLEST.VGTSV
Retrocopy DSNNIKEVLLFPAMKPEDKKENVAPTETLEST-VGTSV

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	0.13 RPM	29.71 RPM
SRP051959_heart	0.16 RPM	37.71 RPM
SRP051959_kidney	0.16 RPM	35.70 RPM
SRP051959_liver	0.04 RPM	42.04 RPM
SRP051959_lung	0.11 RPM	32.99 RPM
SRP051959_lymph_node	0.07 RPM	35.57 RPM
SRP051959_skeletal_muscle	0.17 RPM	93.95 RPM
SRP051959_spleen	0.06 RPM	32.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_608 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_608 has 0 orthologous retrocopies within eutheria group .

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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,