RetrogeneDB ID: retro_cjac_3875

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285608.1:2277..3353(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003068
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSCJAG00000019739
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_cjac_3875
ATGGCGGCGGTGTCTGGCTTGGTGCGGAGACACCTTCGCCAGGTCTCCGGGCAGCTGAAGAGGCGCTTTCATAGGACCGC
GCCGGCTGCGCTGCAGGTGACAGTTCATGATGCTATAAATCAGGGCATGGATGAGGAGCTGGAAAGAGATAGAAGGTATT
TCTCCTTGGAGAAGAAGTTGCCCAGTACGATGGGGCATACAAGGTTAGTCGAGGGCTATGGAAGAAATATGGAGACAAGA
GGATTATTGACACTCCCATATCAGAGATGGGCTTTGCTGGAATTGCTGTAGGTGCAGCTATGGCTGGGTTGCGGCCCATT
TGTGAATTTATGACCTTCAATTTCTCCATGCAAGCCATTGACCAGGTTATAAACTCAGCTGCCAAGACCTACTACATGTC
CGGTGGCCTTCAGTCTGTGCCTATAGTCTTCAGGGGGCCCAATGGTGCCTCAGCAGGTGTAGCTGCCCAGCACTCACAGT
GCTTTGCTGCATGGTATGGGCACTGCCCAGGCTTAAAGGTGGTCAGTCCCTGGAATTCAGAGGATGCTAAAGGACTTATT
AAATCAGCCATTCGGGATAACAATCCAGTGGTGGTGCTAGAAAATGAATTGATGTATGGGGTTCCTTTTGAATTTCCTCC
GGAAGCGCAGTCAAAAGATTTCCTAGTTCCTATTGGAAAAGCCAAAATAGAAAGGCAAGGAACACATATAACTGTGGTTT
CCCATTCGAGACCTGTGGGCCACTGCTTAGAAGCTGCAGCAGTGCTATCTAAAGAGGGAGTTGAATGTGAGGTGATAAAT
ATGCGTACCATCAGACCAATGGACATGGAAACCATAGAAGCCAGTGTCATGAAGACAAATCACCTTGTAACTGTGGAAGG
AGGCTGGCCACAGTTTGGAGTAGGAGCTGAAATCTGTGCCAGGATCATGGAAGGTCCTGCATTCAATTTCCTGGATGCTC
CTGCTGTTCGTGTCACTGGTGCTGATGTCCCTATGCCTTATGCAAAGATTCTGGAAGACAACTCTATACCTCAGGTCAAA
GACATCATATTTGCAATAAAGAAAACATTAAATATT

Alignment

ORF - retro_cjac_3875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVSGLVRRPLRQVSGLLKRRFHRTAPAALQVTVRDAINQGMDEELERDE-KVFLLGEEVAQYDGAYKV
          MAAVSGLVRR.LRQVSG.LKRRFHRTAPAALQVTV.DAINQGMDEELERD..KVFLLGEEVAQYDGAYKV
Retrocopy MAAVSGLVRRHLRQVSGQLKRRFHRTAPAALQVTVHDAINQGMDEELERDR<KVFLLGEEVAQYDGAYKV

Parental  SRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQS
          SRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQS
Retrocopy SRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQS

Parental  VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP
          VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP
Retrocopy VPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP

Parental  FEFPPEAQSKDFLVPIGKAKIERQGTHITVVSHSRPVGLILMKEFKVKEDWLGSEVINMRTIRPMDMETI
          FEFPPEAQSKDFLVPIGKAKIERQGTHITVVSHSRPVG..L.............EVINMRTIRPMDMETI
Retrocopy FEFPPEAQSKDFLVPIGKAKIERQGTHITVVSHSRPVGHCLEAAAVLSKEGVECEVINMRTIRPMDMETI

Parental  EASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSIPQVKDI
          EASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSIPQVKDI
Retrocopy EASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSIPQVKDI

Parental  IFAIKKTLNI
          IFAIKKTLNI
Retrocopy IFAIKKTLNI

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	2.44 RPM	8.61 RPM
SRP051959_heart	9.88 RPM	28.19 RPM
SRP051959_kidney	6.83 RPM	24.09 RPM
SRP051959_liver	9.81 RPM	32.14 RPM
SRP051959_lung	2.36 RPM	9.30 RPM
SRP051959_lymph_node	2.56 RPM	10.46 RPM
SRP051959_skeletal_muscle	8.98 RPM	29.13 RPM
SRP051959_spleen	2.25 RPM	9.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3875 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875 ,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,