RetrogeneDB ID: retro_cjac_3034

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:144953861..144954839(-)
• Located in intron of: ENSCJAG00000002717

Retrocopy information

• Ensembl ID: ENSCJAG00000022502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHF6
• Ensembl ID: ENSCJAG00000004238
• Aliases: None
• Description: PHD finger protein 6 [Source:HGNC Symbol;Acc:18145]

Sequence

>retro_cjac_3034
ATGTCAAGCTCAGTTGAACAGAAAAAAGGGCCTACAAGACAGCGCAAATGTGGCTTTTGTAAGTCAAATAGAGACAAGGA
ATGTGGACAGTTACTAATATCTGAAAACCAGAAGGTGGCAGCGCACCATAAGTGTATGCTCTTTTCATCTGCTTTGGTAT
CATCACACTCTGATAATGAAAGTCTTGGTGGATTTTCTATTGAAGATGTCCAAAAGGAAATTAAAAGAGGCACGACGCTG
ATGTGTTCTTTGTGCCGTTGTCCTGGAGCAACAATTGGTTGTGATGTGAAAACATGTCACAGGACATACCACTACCACTG
TGCATTGCATGATAAAGCTCAAATAGGAGAGAAACCTTCACAAGGAATTTACGTGGTCTATTGCCGAAAACACAAGAAAA
CTGCACATAACTCTGAAGCAGCTGATTTAGAGGAAGGTTTTAATGAACATGAACTGGAGCCCTCATCACCTAAAAGTAAA
AAGAAAAGTCGCAAAGGAAAGCCAAGAAAAACTAATTTTAAAGGGCTGTCAGAAGATACCAGGTCCACATCCTCCCACGG
AACAGATGAAATGGAAAGTAGTTCCTATAGAGATAGGTCTCCACACAGAAGCAGCCCTAGTGACACCAGGCCTAAATGTG
GATTTTGCCATGTTGGGGAGGAGGAAAATGAAGCACGAGGAAAGCTGCATATATTTAATGCCAAGAAGGCAGCTGCCCAT
TATAAGTGCATGTTGTTTTCTTCTGGCACAGTCCAGCTCACAACAACATCAAGAGCAGGATTTGGAGACTTTGATATTAA
AACTGTACTTCAGGAGATTAAGCGAGGAAAAAGAATGAAATGTACACTTTGCAGTCAGCCTGGTGCTACTATTGGATGTG
AAATAACAGCCTGTGTTAAGACTTACCATTACCACTGTGGAGTACAAGACAAAGCTAAATACATTGAAAATATGTCACGA
GGAATTTACAAATATTGG

Alignment

ORF - retro_cjac_3034 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.63 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSSVEQKKGPTRQRKCGFCKSNRDKECGQLLISENQKVAAHHKCMLFSSALVSSHSDNESLGGFSIEDV
          MSSSVEQKKGPTRQRKCGFCKSNRDKECGQLLISENQKVAAHHKCMLFSSALVSSHSDNESLGGFSIEDV
Retrocopy MSSSVEQKKGPTRQRKCGFCKSNRDKECGQLLISENQKVAAHHKCMLFSSALVSSHSDNESLGGFSIEDV

Parental  QKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYHCALHDKAQIREKPSQGIYMVYCRKHKKTAHNSEA
          QKEIKRGT.LMCSLC.CPGATIGCDVKTCHRTYHYHCALHDKAQI.EKPSQGIY.VYCRKHKKTAHNSEA
Retrocopy QKEIKRGTTLMCSLCRCPGATIGCDVKTCHRTYHYHCALHDKAQIGEKPSQGIYVVYCRKHKKTAHNSEA

Parental  -DLEESFNEHELEPSSPKSKKKSRKGRPRKTNFKGLSEDTRSTSSHGTDEMESSSYRDRSPHRSSPSDTR
          .DLEE.FNEHELEPSSPKSKKKSRKG.PRKTNFKGLSEDTRSTSSHGTDEMESSSYRDRSPHRSSPSDTR
Retrocopy ADLEEGFNEHELEPSSPKSKKKSRKGKPRKTNFKGLSEDTRSTSSHGTDEMESSSYRDRSPHRSSPSDTR

Parental  PKCGFCHVGEEENEARGKLHIFNAKKAAAHYKCMLFSSGTVQLTTTSRAEFGDFDIKTVLQEIKRGKRMK
          PKCGFCHVGEEENEARGKLHIFNAKKAAAHYKCMLFSSGTVQLTTTSRA.FGDFDIKTVLQEIKRGKRMK
Retrocopy PKCGFCHVGEEENEARGKLHIFNAKKAAAHYKCMLFSSGTVQLTTTSRAGFGDFDIKTVLQEIKRGKRMK

Parental  CTLCSQPGATIGCEIKACVKTYHYHCGVQDKAKYIENMSRGIYKLY
          CTLCSQPGATIGCEI.ACVKTYHYHCGVQDKAKYIENMSRGIYK..
Retrocopy CTLCSQPGATIGCEITACVKTYHYHCGVQDKAKYIENMSRGIYKYW

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	6.77 RPM	14.00 RPM
SRP051959_heart	7.23 RPM	13.35 RPM
SRP051959_kidney	10.25 RPM	21.25 RPM
SRP051959_liver	7.45 RPM	10.09 RPM
SRP051959_lung	11.68 RPM	21.47 RPM
SRP051959_lymph_node	7.90 RPM	30.52 RPM
SRP051959_skeletal_muscle	3.67 RPM	8.89 RPM
SRP051959_spleen	10.11 RPM	22.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3034 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3034 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004238	1 retrocopy	retro_cjac_3034 ,
Callithrix jacchus	ENSCJAG00000008839	1 retrocopy	retro_cjac_2944,
Oryctolagus cuniculus	ENSOCUG00000007022	1 retrocopy	retro_ocun_1670,