RetrogeneDB ID: retro_cjac_2970

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:24621620..24623785(-)
• Located in intron of: ENSCJAG00000004914

Retrocopy information

• Ensembl ID: ENSCJAG00000004996
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KAT2B
• Ensembl ID: ENSCJAG00000003744
• Aliases: None
• Description: None

Sequence

>retro_cjac_2970
TGGAAAAACCCCAACCCCTCACCCACTCTCCCCAGAGCCGATCTGCAGCAAATATTTGTCAGTCTAATGAATCCTGTCGG
AGTTGTAGCCATGCCCTAGCTGCTCAGGTTTCCCACCTGGAGAATGTGTCAGAGGAAGAAATGAACAGACTCCTGGGAAT
AGTGTTGGATGTGGAATATCTCTTTACCTGTGTCCACAAGGAAGAAGATGCAGATACCAAGCAAGTTTATTTCTACCTAT
TTAAGCTCTTGAGAAAGTCTATTTTACAAAGAGGAAAACCTGTGGTTGAAGGCTCTTTGGAAAAGAAACCCCCATTTGAA
AAACCTAGCATTGAACAGGGTGTGAATAACTTCGTACAGTACAAATTTAGTCACCTGCCAGCAAAAGAAAGGCAAACAAT
AGTTGAGCTGGCAAAAATGTTCCTAAACCGGATCAACTATTGGCACCTGGAAGCACCATCTCAACGAAGACTGCGATCGC
CCAATGATGTTATTTCTGGATACAGGGAGAATTACACAAGGTGGCTGTGTTACTGCAACGTTCCACAGTTCTGCGACAGT
CTACCTCGGAACGAAACCACACAGGTGTTTGGGAGAACATTGCTTCGCTCGGTCTTCACGGTTATGAGGCGACAGCTCCT
GGAACAAGCAAGACAAGAAAAAGATCAACTGCCTCTTGAAAAACGAACTCTAATCCTCACCCATTTCCCAAAATTTCTGT
CCATGTTAGAAGAAGAAGTTTATAGTCAAAACTCCCCCATCTGGGATCAGGATTTTCTCTCAGCTTCTTCCAGAACCAGC
CAGCTAGGCATCCAAACAGTTATCAGTCCACCTCCTGTGGCTGGGACAACTTCATACAATTCAACCTCATCTTCCCTTGA
GCAGCCAAATGCAGGGAGCAGCAGTCCTGCCTGCAAAGCCTCTTCTGGACTTGAAGCAAACCCAGGAGAAAAGAGGAAAA
TGACTGATTCTCATATTCTGGAGGAGGCCAAGAAACCCCGAGTTATGGGGGATATTGCGATGGAATTAATCAACGAGGTT
ATGTCTACCATCACGGACGCTGCAGCAATGCTCGGACCAGAGACCAATTTTCTGTCAGCACATTCAGCCAGGGATGAGGC
GGCCAGGTTGGAAGAGCGCAGGGGTGTAATTGAATTCCACGTAGTTGGCAACTCCCTCAACCAGAAACCAAACAAGAAGA
TCCTGATGTGGCTGGTCGGACTTCAGAACGTTTTCTCCCACCAGCTGCCCCGAATGCCAAAAGAATACATCACAGGGCTT
GTCTTTGACCCGAAACACAAAACACTTGCTTTAATTAAAGATGGCCGTGTCATTGGTGGTATCTGTTTCCGTATGGTTCC
ATCTCAAGGATTCACAGAGATTGTCTTCTGTGCTGTAACCTCAAATGAGCAAGTCAAGGGCTATGGAACACATCTGATGA
ATCATTTAACAGAATATCACATAAAACATGACATCCTGAACTTCCTCACATATGCAGATGAGTATGCAATTGGATACTTT
AAGAAACAGGGTTTCTTCAAAGAAATTAAAATACCTAAAACCAAATATGTTGGCTATATCAAGGATTATGAAGGAGCCAC
CTTAATGGGGTGTGAGCTAAATCCACGGATTCCATATACAGAATTTTCTGTCATCATTAAAAAGCAGAAGGAGATCATTA
AAAAGCTGATTGAAAGAAAACAGGCACAGATTCGAAAAGTTTACCTTGGACTTTCATGTTTTAAAGATGGAGTTCGACAG
ATTCCTATAGAAAGCATTCCAGGAATTAGAGAGACAGGCTGGAAACCGAGTGGAAAAGAGAAAAGTAAAGAGCCCAAAGA
CCCTGACCAGCTTTATAGCACACTCAAGAGCATCCTCCAGCAGGTGAAGAGCCATCAAAGCGCTTGGCCCTTCATGGAAC
CTGTGAAGAGAACAGAAGCTCCAGGATATTATGAAGTTATAAGGTTCCCCATGGATCTGAAAACCATGAGTGAACGCCTC
AAGAATAGGTACTACGTGTCTAAGAAATTTTTCATGGCAGACTTACAGCGAGTCTTTACCAATTGCAAAGAGTACAACCT
CCCTGCGAGTGAATACTACAAATGTGCCAATATCCTGGAGAAATTCTTCTTCAGTAAAATTAAGGAAGCTGGATTAATTG
ACAAG

Alignment

ORF - retro_cjac_2970 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WKNPNPSPTPPRADLQQIFVSL-TESCRSCSHALEAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE
          WKNPNPSPT.PRADLQQIFVSL..ESCRSCSHAL.AA.VSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE
Retrocopy WKNPNPSPTLPRADLQQIFVSL<NESCRSCSHAL-AAQVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE

Parental  EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA
          EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA
Retrocopy EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA

Parental  KMFLNR----NLEAPSQRRLRSPNDDISGYKENYTRWLCYCNVPQFCDSLPRYETTQVFGRTLLRSVFTV
          KMFLNR.....LEAPSQRRLRSPND.ISGY.ENYTRWLCYCNVPQFCDSLPR.ETTQVFGRTLLRSVFTV
Retrocopy KMFLNRINYWHLEAPSQRRLRSPNDVISGYRENYTRWLCYCNVPQFCDSLPRNETTQVFGRTLLRSVFTV

Parental  MRRQLLEQARQEKDKLPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP
          MRRQLLEQARQEKD.LPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP
Retrocopy MRRQLLEQARQEKDQLPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP

Parental  PVAGTISYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDIPMELINEVM
          PVAGT.SYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDI.MELINEVM
Retrocopy PVAGTTSYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDIAMELINEVM

Parental  STITDPAAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR
          STITD.AAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR
Retrocopy STITDAAAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR

Parental  MPKEYITRLVFDPKHKTLALIKDGRVIGGICFRMFPSQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHI
          MPKEYIT.LVFDPKHKTLALIKDGRVIGGICFRM.PSQGFTEIVFCAVTSNEQVKGYGTHLMNHL.EYHI
Retrocopy MPKEYITGLVFDPKHKTLALIKDGRVIGGICFRMVPSQGFTEIVFCAVTSNEQVKGYGTHLMNHLTEYHI

Parental  KHDILNFLTYADEYAIGYFKKQGFSKEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE
          KHDILNFLTYADEYAIGYFKKQGF.KEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE
Retrocopy KHDILNFLTYADEYAIGYFKKQGFFKEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE

Parental  IIKKLIERKQAQIRKVYPGLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ
          IIKKLIERKQAQIRKVY.GLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ
Retrocopy IIKKLIERKQAQIRKVYLGLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ

Parental  VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESE
          VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKK.FMADLQRVFTNCKEYN.P.SE
Retrocopy VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKFFMADLQRVFTNCKEYNLPASE

Parental  YYKCANILEKFFFSKIKEAGLIDK
          YYKCANILEKFFFSKIKEAGLIDK
Retrocopy YYKCANILEKFFFSKIKEAGLIDK

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	1.06 RPM	12.05 RPM
SRP051959_heart	2.19 RPM	29.77 RPM
SRP051959_kidney	1.44 RPM	18.88 RPM
SRP051959_liver	2.19 RPM	33.38 RPM
SRP051959_lung	3.20 RPM	42.47 RPM
SRP051959_lymph_node	2.40 RPM	28.01 RPM
SRP051959_skeletal_muscle	2.05 RPM	24.96 RPM
SRP051959_spleen	2.48 RPM	38.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2970 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2970 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2970 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003744	1 retrocopy	retro_cjac_2970 ,
Mus musculus	ENSMUSG00000000708	1 retrocopy	retro_mmus_2669,
Nomascus leucogenys	ENSNLEG00000003459	1 retrocopy	retro_nleu_2812,