RetrogeneDB ID: retro_cjac_3188

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:19862620..19863595(+)
• Located in intron of: ENSCJAG00000005332

Retrocopy information

• Ensembl ID: ENSCJAG00000005330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KLF5
• Ensembl ID: ENSCJAG00000021146
• Aliases: None
• Description: None

Sequence

>retro_cjac_3188
AGTATCAACATGAACGTGTTCCTCCCTGACATCACTCACCTGAGAACTGTCCTCTACAAATCCCAGAGACCCTGCGTCAC
ACACATCAAGACAGAACCTGTTGCCATTTTCAGCCACCAGAGTGAAACGACTGCCCCTCCTCCGGCCCGACCCAGGCCCT
CCCTGAGTTCACCAGTATTATTCAGCTCACACCAGACAGCAGCTCCAGAGGTGAACAATATTTTCCTCAAACAAGAACTT
CCTACACCAGATCTTCATCTTTCTGTCCCTCCCCAGCAGGGCCACCTGTACCAGCTACTGAATACACGGGATCTAGATAT
GCCCAGTTCTGCAAACCAGACAGCAGCAATGGACATTGTTAATGTTTCTATGTCAGCTGCCTTGGCAGGCCTTAACACAC
ACACCTCTGCTGTTCCTCAGACTGCAGTGAAACAGTTCCAGGCCATGCCCCCTTGCACATACACAATACTCAGTCAGTTT
CTTCCACAACAGGCTACTTACTTTCCCCCGTCACCACCAAGCTCAGAGCCTGGAAGTCCAGATAGACAAGCAGAGATGCT
CCAGAATTTAACCCCACCTCCATCCTATGCTGCTATAATTGCTTCTAAACTGGCAATTCAGCATCCAAATTTACCCACCA
CCCTGCCAGTTAACTCACAAAACATCCAACCTGTCAGATACAATAGAAGGAGTAACCCTGATCTGGAGAAACGACGCATT
CACTACTGCGATTACGCTGGTTGCACAAAAGTTTATACAAAGTCTTCTCATTTAAAAGCTCACCTGAGGACTCACACTGG
TGAAAAGCCATACAAGTGCACCTGGGAAGATTGCGACTGGAGGTTCGCGAGATCCGATGAGCTGACCCGCCACTACCGGA
AGCACACGGGCTCCAAGCCCTTCCAGTGCAGGGTGTGCAACCGCAACTTCTCACGCTCTAACCACCTGGCCCTGCACATG
AAGAGGCACCAGAAC

Alignment

ORF - retro_cjac_3188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 71.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SINMNVFLPDITHLRTGLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPA-PTQALPEFTSI-FSSHQTAA
          SINMNVFLPDITHLRT.LYKSQRPCVTHIKTEPVAIFSHQSETTAPPPA.PTQALPEFTSI.FSSHQTAA
Retrocopy SINMNVFLPDITHLRTVLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPA<PTQALPEFTSI>FSSHQTAA

Parental  PEVNNIFIKQELPTPDLHLSVPPQQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAV
          PEVNNIF.KQELPTPDLHLSVPPQQGHLYQLLNT.DLDMPSS.NQTAAMD..NVSMSAA.AGLNTHTSAV
Retrocopy PEVNNIFLKQELPTPDLHLSVPPQQGHLYQLLNTRDLDMPSSANQTAAMDIVNVSMSAALAGLNTHTSAV

Parental  PQTAVKQFQAMPPCTYTMPSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHN
          PQTAVKQFQAMPPCTYT..SQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAA.IASKLAI..
Retrocopy PQTAVKQFQAMPPCTYTILSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAAIIASKLAIQH

Parental  PNLPTTLPVNSQNIQPVRYNRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGC
          PNLPTTLPVNSQNIQPVRYNRRSNPDLEKRRIHYCDY.GCTKVYTKSSHLKAHLRTHTGEKPYKCTWE.C
Retrocopy PNLPTTLPVNSQNIQPVRYNRRSNPDLEKRRIHYCDYAGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEDC

Parental  DWRFARSDELTRHYRKHTGAKPFQCGVCNRSFSRSDHLALHMKRHQN
          DWRFARSDELTRHYRKHTG.KPFQC.VCNR.FSRS.HLALHMKRHQN
Retrocopy DWRFARSDELTRHYRKHTGSKPFQCRVCNRNFSRSNHLALHMKRHQN

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	0.02 RPM	65.05 RPM
SRP051959_heart	0.00 RPM	3.00 RPM
SRP051959_kidney	0.00 RPM	4.53 RPM
SRP051959_liver	0.02 RPM	0.65 RPM
SRP051959_lung	0.07 RPM	19.54 RPM
SRP051959_lymph_node	0.02 RPM	1.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.79 RPM
SRP051959_spleen	0.00 RPM	3.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3188 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009798	1 retrocopy	retro_chof_1208,
Callithrix jacchus	ENSCJAG00000021146	1 retrocopy	retro_cjac_3188 ,
Nomascus leucogenys	ENSNLEG00000016120	1 retrocopy	retro_nleu_65,
Pan troglodytes	ENSPTRG00000039565	2 retrocopies	retro_ptro_111, retro_ptro_2968,