RetrogeneDB ID: retro_cjac_1925

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:74589874..74591022(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014390
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUGP1
• Ensembl ID: ENSCJAG00000005755
• Aliases: SUGP1, SF4
• Description: None

Sequence

>retro_cjac_1925
AAGGCCTATGGGTGGTTTGGAGTTTCTCCCCCTAAATCTGGAAAAATGAACATGAACATCCTTCACCAAGAAGAGCTCAA
TGCTCAGAAGAAAGGGGAAATTGAAGCCAAAATGGAACAGAAAGCCAAGCAGAATCAGGGGCCAGCCCTCAGTCCCCACA
TCCCAGAGAAATCTCAAATGCACACAACTCTTCCTGCCTTTCCAACAAGTTCGCTAACGACAGTCATTTACTGCAGCAGT
TTTTGAAGTTGCAGAAGGCACAGACCAGCACAGATGCCGGCCCCCACCCCCTACCCAGTGCGCCCACTGCCCCTTCCAGC
ACACTTACCCCCAGTGCAGGAAAGGGGTCCCTCCTCATCAGCAAGCATACAGGCCTGGGGCTGGCCAGCTCCCCGGGCCA
GGTGACGAGCTCTCGCAGTCAAGCAGCTGCTGGTGGCGCACTGTCTGAGTGTCTTCCAGTACCCGGAAGAGAAGGAGGAG
GACTATGAGCAGTGGCTGAAAATCAAACTTTCACTCCCAGAAGGAATCGAGACTCGGAAAATGATAGAGAAATTGGCCCA
CTTTGTGGCAGAGGAGTTAGAAAAAGAAGCTATGGAGGATTACAAGGATAACCCTGCGTTTGCATTTTTGCCTGATAAAG
AATAGCAGGGAATTCCTCTACTACAGAAAGAAGGTGGCTGAGGTAAGAAAGGAAGCGCAGAAGTCCCCGGCAGCCTCTCA
GAAAGTTTCACCCCCAGAGGACGTAGAGGTCAAGAACCTTGCAGAGAACTTGGCCAGGTTCATAGCAGGCAGGGATCCCG
AGTGGAAACCATCACCCTCCAGAACCATCATGAAAATCAGGCATTCAGCTTTCTGTACAAGCCCAACAGCCAAGGGTACA
AGTGCTACTGACAGAAGCTGGAGGAGTTCCAGAAAGCCAAGGCCGGCTCCCCAGGCAACCTCATGGCACAGGACACGGCC
TGAAGCGCAAGTCCTCTCCTGAGGCCTGACCCCAGCCACCACCTGCCCCGCCTCCTCCTCGCCTGTGCCGCCCCCACCCC
CCTACACCCCCACACACACCCCCACCCCCGCTCGTCATACCTGCTCCAGCCACCCCCGGGAAGCCAGACTCCCTCTGCAA
CCACTGTGAAGAGAAAGCAGAAGAGCCG

Alignment

ORF - retro_cjac_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 60.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KANRWFGVAPPKSGKMNMNILHQEELIAQKKREIEAKMEQKAKQNQV-ASPQPPHPGEITNAHNSSCVSN
          KA..WFGV.PPKSGKMNMNILHQEEL.AQKK.EIEAKMEQKAKQNQ..ASPQ.PHP.EI.NAHNSSC.SN
Retrocopy KAYGWFGVSPPKSGKMNMNILHQEELNAQKKGEIEAKMEQKAKQNQG<ASPQSPHPREISNAHNSSCLSN

Parental  KFANDGSFLQQFL---KLQKSQTSTDTPA-STPIVPPSTPTPSAGKRSLLISRRTGLGLAS-LPGPVKSY
          KFAND...LQQFL...K.Q.S......P..S.P..P.ST.TPSAGK.SLLIS..TGLGLAS.LPGP....
Retrocopy KFANDSHLLQQFLKLQKAQTSTDAGPHPLPSAPTAPSSTLTPSAGKGSLLISKHTGLGLAS<LPGPGDEL

Parental  SHA-KQLPVAHRPSVFQSPDEDEEEDYEQWLEIKVSPPEGAETRKVIEKLARFVAEGGPELEKVAMEDYK
          S...KQL.VAH..SVFQ.P.E..EEDYEQWL.IK.S.PEG.ETRK.IEKLA.FVAE...ELEK.AMEDYK
Retrocopy SQS<KQLLVAHCLSVFQYPEE-KEEDYEQWLKIKLSLPEGIETRKMIEKLAHFVAE---ELEKEAMEDYK

Parental  DNPAFAFLHD-KNSREFLYYRKKVAEIRKEAQKSQAASQKVSPPEDEEVKNLAEKLARFIADGGPE-VET
          DNPAFAFL.D.KNSREFLYYRKKVAE.RKEAQKS.AASQKVSPPED.EVKNLAE.LARFIA...PE.VET
Retrocopy DNPAFAFLPD>KNSREFLYYRKKVAEVRKEAQKSPAASQKVSPPEDVEVKNLAENLARFIAGRDPE<VET

Parental  IALQNNRENQAFSFLYEPNSQGYKYYRQKLEEFRKTKAGSTGTLTALDPS-LKRKSPPEALSGSLPPATT
          I.LQN..ENQAFSFLY.PNSQGYK.Y.QKLEEF.K.KAGS.G.L.A.D...LKRKS.PEA.....P.A..
Retrocopy ITLQNHHENQAFSFLYKPNSQGYKCY*QKLEEFQKAKAGSPGNLMAQDTA<LKRKSSPEA*PQPPP-APP

Parental  CPASSTPAPTITPAPAVSGKPASAATVKRKRKSRWGPEEDKVELP
          .P....P.P...P..........A.....K..S.....E.K.E.P
Retrocopy PPRLCRPHPPTPPHTPPPPLVIPAPATPGKPDSLCNHCEEKAEEP

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	7.14 RPM
SRP051959_heart	0.00 RPM	9.72 RPM
SRP051959_kidney	0.00 RPM	8.99 RPM
SRP051959_liver	0.00 RPM	5.20 RPM
SRP051959_lung	0.00 RPM	9.60 RPM
SRP051959_lymph_node	0.00 RPM	11.99 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.45 RPM
SRP051959_spleen	0.00 RPM	9.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1925 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005755	1 retrocopy	retro_cjac_1925 ,
Macaca mulatta	ENSMMUG00000028834	1 retrocopy	retro_mmul_2040,