RetrogeneDB ID: retro_cjac_419

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:76148922..76150333(+)
• Located in intron of: ENSCJAG00000011461

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KRT7
• Ensembl ID: ENSCJAG00000017950
• Aliases: None
• Description: None

Sequence

>retro_cjac_419
ATGTCCATCCACTTCAGCTCCCTGCTGTTCAGCTCGCGCTCCGCCGGCTTCTCCGGCCGCTGTGCCCAGGTGCGCCTGAG
CTCCACGCACCCCGGTGGCTTCGGCAGCAGCAGCCTCTACGGCCTGGGCGCCTCGCCGCTGCGCGTGACCATGCGCTCCG
CCTATGGGGGCCCGGTGGGCGACGGCATCCGCGAGGTCACCATCAACCAGAGCCTGCTGGCCCCGCTGCGGCTGGACACA
GACCCCTCCCTCCAGCGGGTGCGCCAGGAGGAGCGTGAGCGGATCAAGACCCTCAACAAGTTTGCCTCCTTCATCGACAA
GGTGCGTTTTCTGGAGCAGCAGAACAAGCTGCTGGAGACCAAGTGGGCGCTGCTGCAGGAGCAGAAGTCAGCCAAGAGCA
GCCGCCTCCCAGACATCTTTGAAGCCCAGATTTTCTGGCCTTAGGGGGCAGCTTGAGGCGCTGCAGGTGGATGGGAGCCG
CCTAGAGGCGGAGCTGCGGAGCATGCGGGATATGGTGGAGGACTTCAAGAATAAATACGAAGATGAAATTAACCACCGCA
CGGCTGCTGAGAATGAGTTTGTGGTGCTGAAGAAGGATGTGGGTGCTGCCTACATGAGCAAGGTGGAGCTGGAGGCCAAG
GTGGTCGCCCTGAATGATGAGATCAACTTCCTCAGGACCCTCCATGAGACGGAGTTGACAGAGCTGCAGTCACAGATCTT
GGACACGTCCGTGGTGCTGTCCATGGACAACAGCCGCTCCCTGGACCTAGACGGCATCATCGCCGAGGTCAAGGCTCAGT
ACGAGGAGATGGCCAAGTGCAGCCGGGCTGAGACCGAAGCCTGGTACCAGACCAAGTTTGAGACCCTCCAGGCCCAGGCT
GGGAAGCATGGGGATGATCTACGGAATACCCGGAGCGAGATTGCAGAGATGAACCGGGCCATCCAGAGGCTGCAGGCTGA
GATCGACGCCATCAAGAACCAGCGTGCCAAGTTGGAGGCCGCCATTGCTGAGGCTGAGGAGCGTGGGGAGCTGGCACTCA
AGGATGCTCGTGCCAAGCAGGAGGAGCTGGAGGCTGCCCTGCAGCGGGCCAAGTAAGACATGGCACGGCAGCTGCGTGAG
TACCAGGAGCTGATGAGCGTCAAGCTGGCCCTGGACATCGAGATTGCCACATACCGCAAGCTGTTGGAGGGGGAGAAGAG
CCGGTTGGCCGGAGATGGAGTGGGAGCCGTGAATATCTCTGTGGTGAATTCCACTGGAGGCAGTGGCAGTGGCAGTGGTG
GTGGCATTGGGCTGAGCTTCGGGGGAACCATGGGCAGCAATGCCCTGAGCTTCTCCAGCAGTGCGGGTCCTGGGGCCCTG
AAGGCTTATTCCATCCGGACCACATCCACCAGTCGCAGGAGCGCCCACAAC

Alignment

ORF - retro_cjac_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIHFSSPLFSSRSAGFSGRGAQVRLSSARPGGFGSSSLYGLGASRPRVNMRSAYGGPVGAGIREVTINQ
          MSIHFSS.LFSSRSAGFSGR.AQVRLSS..PGGFGSSSLYGLGAS..RV.MRSAYGGPVG.GIREVTINQ
Retrocopy MSIHFSSLLFSSRSAGFSGRCAQVRLSSTHPGGFGSSSLYGLGASPLRVTMRSAYGGPVGDGIREVTINQ

Parental  SLLAPLRLDTDPSLQRVRQEEREQIKTLNNKFASFIDKVRFLEQQNKLLETKWALLQEQKSAKSSRLPDI
          SLLAPLRLDTDPSLQRVRQEERE.IKTLN.KFASFIDKVRFLEQQNKLLETKWALLQEQKSAKSSRLPDI
Retrocopy SLLAPLRLDTDPSLQRVRQEERERIKTLN-KFASFIDKVRFLEQQNKLLETKWALLQEQKSAKSSRLPDI

Parental  FEAQI-AGLRGQLEALQVDGGRLEVELRSMQDVVEDFKNKYEDEINRRTAAENEFVVLKKDVDAAYMSKV
          FEAQI..GLRGQLEALQVDG.RLE.ELRSM.D.VEDFKNKYEDEIN.RTAAENEFVVLKKDV.AAYMSKV
Retrocopy FEAQI>SGLRGQLEALQVDGSRLEAELRSMRDMVEDFKNKYEDEINHRTAAENEFVVLKKDVGAAYMSKV

Parental  ELEAKVVALNDEINFLRTLHETELTELQSQISDTSVVLSMDNSRSLDLDGIIAEVKAQYEEMAKCSRAEA
          ELEAKVVALNDEINFLRTLHETELTELQSQI.DTSVVLSMDNSRSLDLDGIIAEVKAQYEEMAKCSRAE.
Retrocopy ELEAKVVALNDEINFLRTLHETELTELQSQILDTSVVLSMDNSRSLDLDGIIAEVKAQYEEMAKCSRAET

Parental  EAWYQTKFETLQAQAGKHGDDLRNTRSEIAEMNRAIQRLQAEIDAIKNQRAKLEAAIAEAEERGELALKD
          EAWYQTKFETLQAQAGKHGDDLRNTRSEIAEMNRAIQRLQAEIDAIKNQRAKLEAAIAEAEERGELALKD
Retrocopy EAWYQTKFETLQAQAGKHGDDLRNTRSEIAEMNRAIQRLQAEIDAIKNQRAKLEAAIAEAEERGELALKD

Parental  ARAKQEELEAALQRAKQDMARQLREYQELMSVKLALDIEIATYRKLLEGEESRLAGDGVGAVNISVVNST
          ARAKQEELEAALQRAK.DMARQLREYQELMSVKLALDIEIATYRKLLEGE.SRLAGDGVGAVNISVVNST
Retrocopy ARAKQEELEAALQRAK*DMARQLREYQELMSVKLALDIEIATYRKLLEGEKSRLAGDGVGAVNISVVNST

Parental  GGSGSGSGGGIGLSFGGTMGSNALSFSSSAGPGALKAYSIRTTSTSRRSARN
          G...........LSFGGTMGSNALSFSSSAGPGALKAYSIRTTSTSRRSA.N
Retrocopy GXXXXXXXXXXXLSFGGTMGSNALSFSSSAGPGALKAYSIRTTSTSRRSAHN

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	1.40 RPM	63.68 RPM
SRP051959_heart	1.12 RPM	5.12 RPM
SRP051959_kidney	1.26 RPM	48.10 RPM
SRP051959_liver	0.71 RPM	2.40 RPM
SRP051959_lung	1.92 RPM	31.14 RPM
SRP051959_lymph_node	1.85 RPM	0.32 RPM
SRP051959_skeletal_muscle	1.48 RPM	0.52 RPM
SRP051959_spleen	1.64 RPM	0.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_419 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_419 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017950	2 retrocopies	retro_cjac_419 , retro_cjac_648,
Callithrix jacchus	ENSCJAG00000018147	3 retrocopies	retro_cjac_124, retro_cjac_167, retro_cjac_216,
Nomascus leucogenys	ENSNLEG00000017758	2 retrocopies	retro_nleu_593, retro_nleu_726,
Tursiops truncatus	ENSTTRG00000002820	2 retrocopies	retro_ttru_722, retro_ttru_865,