RetrogeneDB ID: retro_cjac_996

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:84062935..84064333(+)
• Located in intron of: ENSCJAG00000036372

Retrocopy information

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

Parental gene information

• Parental gene symbol: EPRS
• Ensembl ID: ENSCJAG00000003457
• Aliases: EPRS, QARS
• Description: None

Sequence

>retro_cjac_996
CGTTTCAACATGGGGCTGCTGATGGGAGAGGCTCAGACTGTGCTCAAGTGGGCAGATGGCAAAATGATCAAGAATGAAGT
GGACATGCAGGTCCTCCACCTTCTGGGTCCCAAGATGGAGGCTGATCTGGAGAAGAAGCCCAAGGTGGCCAAAGCACAGC
TGGAAGAAACAGACTGGAGGACAGCAAAAGATGTGATAGATAATAGTGAGACTGCTGACCAGACCCTGTCTCTGATGGAG
CAGCTCCAGGGGGATGCCCTTAAGTTCCACAAGCCTGACGAGAACTACAAGACCCCAGGCTATGTGATGACTCCACACAC
CATTAATCTACTAAAGCAGCATCTGGAGATTACTGGTGGGCAGGTACTTACCCAGTTCCTGCCAGAACCCAATGGAATCC
TGCATATTGGACATGCCAAAGCCATCACTTTCAACTTTGGCTATGCCAGGGCCAACAATGGCATCTGTTTTCTGTGCTTT
GATGACACCAACCCTGAGAAGGAGGAAGCAAAGTTCTTCACTGCCATCTATGACATGGTGGCCTGGCTGGGTTACACACC
TTACAGAGTGACATATGCCTCTGACTATTTTGACCAGCTATATGCCTGGGCTGTGGAGCTCATTCACAGGGGTCTGGCTT
ATGTGTGTCACCAGTGAGGGGAGGAGCTCAAAGGCCATGATCCTCTGCCCTCACCCTGGAGAGACCGTCCCATGGAGGAG
TCACTGCTGGTCTTTGAGGCAATGCACAAGGGCAAGTTTTCAGAAGGTGAGGCCACACTACAGATGAAGCTAGTGATACA
GGATGGCAAGATGAACCCTGTAGCCTATCGAATCAAGTATACACCACACCACCGCACAGAAGAAAAATGGTGCATCTATC
CCTCCTACAACTACACACACTGATTCTGTGACTCCATCGAGCACATCACTCACTTACTCTGCACCAAGGAATTCCAGGCC
CAATGCTCTTCTTACTTCTGGCTTTGCAGTGCACTAGACGTCTATTGCCCTGTTCAGTGGGAGTATGGCCATCTCAACCT
GCACTATGCTGTTGACTCTAAGGGGAAGATCCTCCAGCTTGTAGCAACTGGTGCTGTGCAGGACTGGGATGACCCACGGC
TCTTTACATGCACGGCCCTGCAACGATGGGGTTTCCCACCTGAGGGCATCAACAACTTCTGTGCCCGGGTGGGAGTGACA
GTGGCACAGACCACAATGGAGCCACATCTTCTAGAAGCCTGTGTGCGTGATGGGCTGAAAGACACAGCCCCATGAGCCAT
GGCTGTGCTGGAGTCACTATGGGTCACCATCACCAACTTTCCCTCTGCCAAGTCCTTGGACATCCAGGTGCCCAACTTCC
CGGTTGATGAGACCAAAAGCTTCCATCAGGTTTTTTTT

Alignment

ORF - retro_cjac_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.2 %
• Parental protein coverage: 64.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFNMGLLMGEARAVLKWADGKMIKNEVDMQVLHLLGPKMEADLEKKPKVAKARLEETDRRTAKDMIENGE
          RFNMGLLMGEA..VLKWADGKMIKNEVDMQVLHLLGPKMEADLEKKPKVAKA.LEETD.RTAKD.I.N.E
Retrocopy RFNMGLLMGEAQTVLKWADGKMIKNEVDMQVLHLLGPKMEADLEKKPKVAKAQLEETDWRTAKDVIDNSE

Parental  TADQTLSLMEQLRGEALKFHKPGENYKTPGYVMTPHTMNLLKQHLEITGGQVRTRFPPEPNGILHIGHAK
          TADQTLSLMEQL.G.ALKFHKP.ENYKTPGYVMTPHT.NLLKQHLEITGGQV.T.F.PEPNGILHIGHAK
Retrocopy TADQTLSLMEQLQGDALKFHKPDENYKTPGYVMTPHTINLLKQHLEITGGQVLTQFLPEPNGILHIGHAK

Parental  AISFNFGYAKANNGICFLRFDDTNPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELIRR
          AI.FNFGYA.ANNGICFL.FDDTNPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELI.R
Retrocopy AITFNFGYARANNGICFLCFDDTNPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELIHR

Parental  GLAYVCHQRGEDLKGHNPLPSPWRDRPMEESLLLFEAMRKGKFSEGEATLRMKLLMEDGKMDPVAYRVKY
          GLAYVCHQ.GE.LKGH.PLPSPWRDRPMEESLL.FEAM.KGKFSEGEATL.MKL...DGKM.PVAYR.KY
Retrocopy GLAYVCHQ*GEELKGHDPLPSPWRDRPMEESLLVFEAMHKGKFSEGEATLQMKLVIQDGKMNPVAYRIKY

Parental  TPHHRTGDKWCIYPTYDYTHCLCDSIEHITHSLCTKEFQARRSSYFWLCNALDVYCPVQWEYGRLNLHYA
          TPHHRT..KWCIYP.Y.YTH..CDSIEHITH.LCTKEFQA..SSYFWLC.ALDVYCPVQWEYG.LNLHYA
Retrocopy TPHHRTEEKWCIYPSYNYTH*FCDSIEHITHLLCTKEFQAQCSSYFWLCSALDVYCPVQWEYGHLNLHYA

Parental  VVSKRKILQLVATGAVRDWDDPRLFTLTALRRRGFPPEGINNFCARVGVTVAQTTMEPHLLEACVRDVLN
          V.SK.KILQLVATGAV.DWDDPRLFT.TAL.R.GFPPEGINNFCARVGVTVAQTTMEPHLLEACVRD.L.
Retrocopy VDSKGKILQLVATGAVQDWDDPRLFTCTALQRWGFPPEGINNFCARVGVTVAQTTMEPHLLEACVRDGLK

Parental  DTAPRAMAVLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPF
          DTAP.AMAVLESL.V.ITNFP.AKSLDIQVPNFP.DETK.FHQV.F
Retrocopy DTAP*AMAVLESLWVTITNFPSAKSLDIQVPNFPVDETKSFHQVFF

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	33.68 RPM
SRP051959_heart	0.00 RPM	23.15 RPM
SRP051959_kidney	0.02 RPM	37.16 RPM
SRP051959_liver	0.04 RPM	34.42 RPM
SRP051959_lung	0.02 RPM	28.52 RPM
SRP051959_lymph_node	0.00 RPM	31.55 RPM
SRP051959_skeletal_muscle	0.00 RPM	29.35 RPM
SRP051959_spleen	0.02 RPM	30.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_996 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_996 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003457	2 retrocopies	retro_cjac_3957, retro_cjac_996 ,
Rattus norvegicus	ENSRNOG00000043447	1 retrocopy	retro_rnor_203,