RetrogeneDB ID: retro_cjac_2154

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:81284724..81286161(+)
• Located in intron of: ENSCJAG00000003780

Retrocopy information

• Ensembl ID: ENSCJAG00000003795
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008375
• Aliases: None
• Description: None

Sequence

>retro_cjac_2154
GCCGAGACTACAACCTCCACCTCGACTCCAGCTGCCCCGACAGCACGGAAGCAGCTGGACAAAGAGCAGGTTAGAAAGGC
ATTGGACGCTCTCTTGACACATTGCAAATCCAGGAAGAACGATTATGGGTTGCTTTTGAATGAGAGTGAAAATGTATTTT
TAATGGTGGTATTATGGAAAATTCCAAGTAAAGAACTGAGGGTCAGATTGCCCTTACCTCATGGTATTCGATCGGATTTA
GAAGATATCTGTTTATTTACGAAGGACGAACCCAATTCAACTCCTGAAAAGACAGAACAGTTCTATAGAAAGCTTTTAAA
CAAGCATGGAATTAAAACCATTTCTCAGATTATCCCCTTCCAAACTCTGAAGAAGGAATATAAACCCTTTGAAGCCAAGC
TCCGCCTTCTGAGCACTTTTGACTTCTTCCTTACTGATGCCAGAATTAGGCGGCTCTTACCCTCACTCATTGGGAGACAT
TTCTATCAAAGAAAAAAAGTTCCAGTATCTGTAAACCTTCTGTCCAAGAATTTATCAAGAGAGATCAATGACTGTATAGG
TGGAACAGTCTTAAACATTTCTAAAAGTGGTTCTTGCAGTGCTATACGCGTTGGTCATGTTGGAATGCAGATTGAGCACA
TCATTGAAAACATTGTTGCTGTCACCAAAGGACTTTCAGAAAAATTGCCAGAGAAGTGGGAGAGCGTGAAACTCCTGTTT
GTGAAAACTGAGAAATCGGCTGCTCTTCCCATCTTTTCCTCGTTCGTCAGCAATTGGGATGAAGCCACCAAAAAATCTAT
GCTTAATAAGAAGAAAAAAGAGGCAAGGAAAAAACGAAGAGAAAGAAATCATGAAAAACAAAAGGAGAGGAACAAAATCA
GAAAGAAGAAACAGGCTAGCAAGGCTGCATCAGTCCTTAGTAAAGACACCGTGACACCTGAAGGTGGTGACGCTACAGTG
GAGAAACCTGAATTGAAGAAGGAGCAGACCCCAGGACATGGGAAGAAAAGGCGTGGCAAAGGAAAAGCTCAAGTTCAAGT
GGCAAATGACTCCGAAGATGAAATTCCGCAGCTGGTACCAATAGGAAAGACTCCAGCTAAGGAGAATGTAGAGATTCAAA
AACATGCCACAGGAAAGAAGTCTCCAAAAAAGAGCCCTATTCCCAGCACACCTCGTGGGAAGAAAAGAAAGGCCTTGCCA
GCATCTGAGACCCCAAAAGCTGCAGAATCTGAGACCCCAGGGAAAGGCCCACAGAAGAAGCCAAAAATCAAAGAAGAGGC
AGTGAAGGAAAAAAATCCTTCGCTGGGGAAAAAAGATGTGAGACAGACTCCTAAAAAGCCAGAGGCCAAGTTCTTCACCA
CTCCTAGTAAATCTTCAAGAAAAACTTCCCACACCCCCAAAAAACGGCCCAAAAAAACCAAAGTACCCCTGTCAACC

Alignment

ORF - retro_cjac_2154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATATSTSTPAAPTARKQLDKEQVRKALDALLTHCKSRKNDYGLLLNESENVFLMVVLWKIPSKELRVRL
          A.T.TSTSTPAAPTARKQLDKEQVRKALDALLTHCKSRKNDYGLLLNESENVFLMVVLWKIPSKELRVRL
Retrocopy AETTTSTSTPAAPTARKQLDKEQVRKALDALLTHCKSRKNDYGLLLNESENVFLMVVLWKIPSKELRVRL

Parental  PLPHGIRSDLEDICLFTKDEPNSTPEKTEQFYRKLLNKHGIKTISQIIPFQTLKKEYKPFEAKLRLLSTF
          PLPHGIRSDLEDICLFTKDEPNSTPEKTEQFYRKLLNKHGIKTISQIIPFQTLKKEYKPFEAKLRLLSTF
Retrocopy PLPHGIRSDLEDICLFTKDEPNSTPEKTEQFYRKLLNKHGIKTISQIIPFQTLKKEYKPFEAKLRLLSTF

Parental  DFFLTDARIRRLLPSLIGRHFYQRKKVPVSVNLLSKNLSREINDCIGGTVLNISKSGSCSAIRVGHVGMQ
          DFFLTDARIRRLLPSLIGRHFYQRKKVPVSVNLLSKNLSREINDCIGGTVLNISKSGSCSAIRVGHVGMQ
Retrocopy DFFLTDARIRRLLPSLIGRHFYQRKKVPVSVNLLSKNLSREINDCIGGTVLNISKSGSCSAIRVGHVGMQ

Parental  IEHIIENIVAVTKGLSEKLPEKWESVKLLFVKTEKSAALPIFSSFVSNWDEATKKSMLNKKKKEARKKRR
          IEHIIENIVAVTKGLSEKLPEKWESVKLLFVKTEKSAALPIFSSFVSNWDEATKKSMLNKKKKEARKKRR
Retrocopy IEHIIENIVAVTKGLSEKLPEKWESVKLLFVKTEKSAALPIFSSFVSNWDEATKKSMLNKKKKEARKKRR

Parental  ERNHEKQKERNKIRKKKQASKAASVLSKDTVTPEGGDATVEKPELKKEQTPGHGKKKRGKGKAQVQVAND
          ERNHEKQKERNKIRKKKQASKAASVLSKDTVTPEGGDATVEKPELKKEQTPGHGKK.RGKGKAQVQVAND
Retrocopy ERNHEKQKERNKIRKKKQASKAASVLSKDTVTPEGGDATVEKPELKKEQTPGHGKKRRGKGKAQVQVAND

Parental  SEDEIPQLVPIGKTPAKENVEIQKHATGKKSPKKSPIPSTPRGKKRKALPASETPKAAESETPGKGPQKK
          SEDEIPQLVPIGKTPAKENVEIQKHATGKKSPKKSPIPSTPRGKKRKALPASETPKAAESETPGKGPQKK
Retrocopy SEDEIPQLVPIGKTPAKENVEIQKHATGKKSPKKSPIPSTPRGKKRKALPASETPKAAESETPGKGPQKK

Parental  PKIKEEAVKEKNPSLGKKDVRQTPKKPEAKFFTTPSKSARKTSHTPKKRPKKTKVPLST
          PKIKEEAVKEKNPSLGKKDVRQTPKKPEAKFFTTPSKS.RKTSHTPKKRPKKTKVPLST
Retrocopy PKIKEEAVKEKNPSLGKKDVRQTPKKPEAKFFTTPSKSSRKTSHTPKKRPKKTKVPLST

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	1.46 RPM	18.57 RPM
SRP051959_heart	0.74 RPM	21.77 RPM
SRP051959_kidney	0.95 RPM	24.98 RPM
SRP051959_liver	0.63 RPM	24.97 RPM
SRP051959_lung	0.96 RPM	22.97 RPM
SRP051959_lymph_node	0.32 RPM	29.57 RPM
SRP051959_skeletal_muscle	0.37 RPM	38.17 RPM
SRP051959_spleen	1.47 RPM	26.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2154 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154 ,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,