RetrogeneDB ID: retro_cjac_4187

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:69381395..69382778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSCJAG00000017832
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608]

Sequence

>retro_cjac_4187
AAGAAGACTGTACCTAAAAAGCAAGTTGTGGCCAAGGCCCCAGTGAAAGCAGCTGCCACCCCAACCCAGAAGAGTTCCAG
CAGTGAGGATTCTTCCAGTGAGGAGGAAGAACAGCAGAAAAAAAACATGAAAAATAAACCAGGTCCGTACAGTTCAGTAT
CCCCACCTTCTGCTCCCCTACCAAAAAAGACCTTGGGAACCCAGCCTCCCAAGAATGCTGTGGAGAAGCACCAGCCTGTG
GAAAGCAGTGAAAACAGCAGCAATGAGTCTGATTCAAGTTCCGAAGAAGAGAAGAAACCCCCAGCTAAGGCAGTTGTCTC
TAAAGCAACCACTAAACCACCTCCAGCAAAGAAAGCAGCAGAGAGCTCTTGAGACAGCTCAGACTCTGACAGCTCTGAGG
ATGATGAAGATCCTTCCAAGCCAGCTGGTACTACCAAGAATTCCTCCAATAAGCCAGCTAGCACCACCAAGTCACCTGCA
GCGAAGCCAGCTGCAGCCCCTAAGCAATCTTTGGGTGGTGGCCAGAAGCCTCTCATGCGAAAGGCTGACAGCAGCTCCAG
TGAGGAAGAGAGCAGCTCCAGTGAGGAGGAGGAGACAAAGAAGACAGTGGCCACCACTAAGCCCAAGGTGACTGCCACAG
CAGCTCCACCTCTGCCTGCCAAGCAGGCTCTTCAGGGTAGTAAGGACAGCAGCTCTGATTCAGACAGCTCCAGCAATGAG
GAGGAGGAGGAAAAGAAGACATCCAAGACCACAGTTAAGAAGCCACAGGAGGTAGCAGGAGGTGCAGCCCCTTCCAAGTC
AGCCTCTGCAAAGAAAGGAAAGGCTGAGAGCAGCAGCAGTTCTTCCTCTGATGATTCCAGTGAGAAGGAAGAAGAGAAGC
CCAAGGGCAAAGGCAAAGGCACTCCAAGACCACAAGCCCTCAAGGCCAACGGCACCTCTGCAATGACTGTCCAGAATGGA
AAAGCAGCTAAGAACAGCGAGGAGGAGGAAGAAAAGAAAAAGGCAGCAGTGGCAGTTTCCAAACCAGGTTCATTAAAGAA
GCGGAAGCAGAATGAGGCTGCCAAGGAGGCTGAGACTCCTCAGGCTAAGAAGATAAAGCTTCAGACCCCTAACACATTTC
CAAAAAGGAAGAAAGGAGAAAAAGGAGCATCATCCCCATTCCGAAGGGTCAGGGAGGAGGAAATTGAGGTGGATTCACGA
GTGGCAGACAACTCCTTTGATGCCAAGCGAGGTGCAGCTGGAGACGGGGGAGAGCGAGCCAATCAGGTTTTGAAGTTCAC
CAAAGGCAAGTCCTTCTAGCATGAGAAAACCAAGAAGAAGTGGGGCAGCTACCAGGGAGGTTCCATCTCTGTTCAGGTCA
ATTCCATGAAGTTTGACAGTGAA

Alignment

ORF - retro_cjac_4187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EETVPKKQVVAKAPVKAAATPTQKSSSSEDSSSEEEEQQKKPMKNKPGPYSSVPPPSAPPPKKTLGTQPP
          ..TVPKKQVVAKAPVKAAATPTQKSSSSEDSSSEEEEQQKK.MKNKPGPYSSV.PPSAP.PKKTLGTQPP
Retrocopy KKTVPKKQVVAKAPVKAAATPTQKSSSSEDSSSEEEEQQKKNMKNKPGPYSSVSPPSAPLPKKTLGTQPP

Parental  KKAVEKQQPVESSEDSSDESDSSSEEEKKSPAKAVVSKATTKPPPAKKAAESSSDSSDSDSSEEDEDPSK
          K.AVEK.QPVESSE.SS.ESDSSSEEEKK.PAKAVVSKATTKPPPAKKAAESS.DSSDSDSSE.DEDPSK
Retrocopy KNAVEKHQPVESSENSSNESDSSSEEEKKPPAKAVVSKATTKPPPAKKAAESS*DSSDSDSSEDDEDPSK

Parental  PAGTTKNSSHKPAGTTKSPAAKPAAAPKQSLGGGQKPLMRKADSSSSEEESSSSEEEKTKKTVATTKPKA
          PAGTTKNSS.KPA.TTKSPAAKPAAAPKQSLGGGQKPLMRKAD...............TKKTVATTKPK.
Retrocopy PAGTTKNSSNKPASTTKSPAAKPAAAPKQSLGGGQKPLMRKADXXXXXXXXXXXXXXETKKTVATTKPKV

Parental  TAKAAPPLPAKQAPQGSRDSSSDSDSSSSEEEEEEKTSKTAVKKKPQEVAGGAAPSKPASAKKGKPESSS
          TA.AAPPLPAKQA.QGS.DSSSDSDSSS.EEEEE.KTSKT.V.KKPQEVAGGAAPSK.ASAKKGK.ESSS
Retrocopy TATAAPPLPAKQALQGSKDSSSDSDSSSNEEEEEKKTSKTTV-KKPQEVAGGAAPSKSASAKKGKAESSS

Parental  SSSSDDSSEEEEEKPKGKGKGTPRPQALKASSTSALTAQNGKAAKNSEEEEEKKKAAVAVSKPGSLKKRK
          SSSSDDSSE.EEEKPKGKGKGTPRPQALKA..TSA.T.QNGKAAKNSEEEEEKKKAAVAVSKPGSLKKRK
Retrocopy SSSSDDSSEKEEEKPKGKGKGTPRPQALKANGTSAMTVQNGKAAKNSEEEEEKKKAAVAVSKPGSLKKRK

Parental  QNEAAKEAETPQAKKIKLQTPNTFPKRKKGEKRASSPFRRVREEEIEVDSRVADNSFDAKRGAAGDWGER
          QNEAAKEAETPQAKKIKLQTPNTFPKRKKGEK.ASSPFRRVREEEIEVDSRVADNSFDAKRGAAGD.GER
Retrocopy QNEAAKEAETPQAKKIKLQTPNTFPKRKKGEKGASSPFRRVREEEIEVDSRVADNSFDAKRGAAGDGGER

Parental  ANQVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSVKFDSE
          ANQVLKFTKGKSF.HEKTKKK.GSY.GGSISVQVNS.KFDSE
Retrocopy ANQVLKFTKGKSF*HEKTKKKWGSYQGGSISVQVNSMKFDSE

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	0.02 RPM	25.47 RPM
SRP051959_heart	0.16 RPM	24.78 RPM
SRP051959_kidney	0.13 RPM	26.91 RPM
SRP051959_liver	0.02 RPM	32.21 RPM
SRP051959_lung	0.15 RPM	29.56 RPM
SRP051959_lymph_node	0.14 RPM	33.90 RPM
SRP051959_skeletal_muscle	0.17 RPM	31.36 RPM
SRP051959_spleen	0.19 RPM	29.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4187 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4187 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187 ,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,