RetrogeneDB ID: retro_cjac_648

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:191377848..191378943(-)
• Located in intron of: None

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_648
AACAAGGTGCGTTTTATGGAGCAGCAGAACAAGCTGCTGGAGACCAAGTGGGCGCTGCTGCAGAAGCAGAAGTCAGCCAA
GAGCAGCCGCCTCCCAGACATCTTTGAGGCCCAGATTGCTGGCCTTAGGGAGCAGCTTGAGGCGCTGCAGGTGGATGGGG
GCTGCCTGGAGGCTGAGCTGCGGAGCATGCAGGATGTGGTGGAGGACTTCAAGAATAAGTACGAAGATGAAATTAACCGC
CGCAGGGCTGCTGAGAATGAGTTTGTGGTGCTGAAGAAGGATGTGGATGCTGCCTACATGAGCAAGGTGGAGCTGGAGGC
CAAGGTGGTTGCCCTGAATGATGAGATCAACTTCCTCAGGACCCTCCATGAGACGGAGTTGACAGAGCTGCAGTCACAGA
TCTCGGACACATCTGTGGTGCTGTACATGGACAACAGTCGCTTTCTGGACCTGGATGGCATCATCACTGAGGTCAAGGCT
CAGTATGAGGAGATGGCCAAATGCAGCTGGACTGAGGCTGAAGCCTGGTACCAGACCAAGTTTGAGACCCTCCAGGCCCA
GGCTGGGAAACATGGGGACGACCTCCGGAATACCTGGAACGAGATTGCAGAGATGAACTGGGCCATCCAGAGGCTGCAGG
CTGAACTCGACGCCATCAAGAACCAGCATGCCAAGTTGGAGGCCGCCATTGCTGAGGCTGAGGAGTGCGGGGAGCTGGCA
CTCAAGGATGCTCGTGCCAAGCAGGAGGAGCTGGAGGCCGCCCTGCAGCGGGCCAAGCAAGACATGGCACGGTAGCGACG
TGAGTACCGGGAGCTGATGAGCGTCAAGCTGGCCCAGGACATCTAGATTGCTACTTACCGCAAGCTGCTGGAGGGCGAGG
AGAGCCGGTTGGCCGGAGATGGAGTGGGAGCCTTGAATATCTCTGTGGTGAATTCCACTGGAGGCACTGGCAGTGGCAGT
GGTGGTGGCATTGGGCTGAGCTGCGGGGGAACCATGGGCAGCAATGCCCTGATCTTCTCCAGCAGTGCGGGTCCTGGGGC
CGCGAAGGCTTATTCCATCCGGACCACATCCACCAGTCACAGGTGCGCCCGCAAC

Alignment

ORF - retro_cjac_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 77.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKVRFLEQQNKLLETKWALLQEQKSAKSSRLPDIFEAQIAGLRGQLEALQVDGGRLEVELRSMQDVVEDF
          .KVRF.EQQNKLLETKWALLQ.QKSAKSSRLPDIFEAQIAGLR.QLEALQVDGG.LE.ELRSMQDVVEDF
Retrocopy NKVRFMEQQNKLLETKWALLQKQKSAKSSRLPDIFEAQIAGLREQLEALQVDGGCLEAELRSMQDVVEDF

Parental  KNKYEDEINRRTAAENEFVVLKKDVDAAYMSKVELEAKVVALNDEINFLRTLHETELTELQSQISDTSVV
          KNKYEDEINRR.AAENEFVVLKKDVDAAYMSKVELEAKVVALNDEINFLRTLHETELTELQSQISDTSVV
Retrocopy KNKYEDEINRRRAAENEFVVLKKDVDAAYMSKVELEAKVVALNDEINFLRTLHETELTELQSQISDTSVV

Parental  LSMDNSRSLDLDGIIAEVKAQYEEMAKCSRAEAEAWYQTKFETLQAQAGKHGDDLRNTRSEIAEMNRAIQ
          L.MDNSR.LDLDGII.EVKAQYEEMAKCS..EAEAWYQTKFETLQAQAGKHGDDLRNT..EIAEMN.AIQ
Retrocopy LYMDNSRFLDLDGIITEVKAQYEEMAKCSWTEAEAWYQTKFETLQAQAGKHGDDLRNTWNEIAEMNWAIQ

Parental  RLQAEIDAIKNQRAKLEAAIAEAEERGELALKDARAKQEELEAALQRAKQDMARQLREYQELMSVKLALD
          RLQAE.DAIKNQ.AKLEAAIAEAEE.GELALKDARAKQEELEAALQRAKQDMAR..REY.ELMSVKLA.D
Retrocopy RLQAELDAIKNQHAKLEAAIAEAEECGELALKDARAKQEELEAALQRAKQDMAR*RREYRELMSVKLAQD

Parental  IEIATYRKLLEGEESRLAGDGVGAVNISVVNSTGGSGSGSGGGIGLSFGGTMGSNALSFSSSAGPGALKA
          I.IATYRKLLEGEESRLAGDGVGA.NISVVNSTGG.GSGSGGGIGLS.GGTMGSNAL.FSSSAGPGA.KA
Retrocopy I*IATYRKLLEGEESRLAGDGVGALNISVVNSTGGTGSGSGGGIGLSCGGTMGSNALIFSSSAGPGAAKA

Parental  YSIRTTSTSRRSARN
          YSIRTTSTS.R.ARN
Retrocopy YSIRTTSTSHRCARN

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	0.64 RPM	63.68 RPM
SRP051959_heart	0.84 RPM	5.12 RPM
SRP051959_kidney	0.84 RPM	48.10 RPM
SRP051959_liver	0.37 RPM	2.40 RPM
SRP051959_lung	1.15 RPM	31.14 RPM
SRP051959_lymph_node	0.34 RPM	0.32 RPM
SRP051959_skeletal_muscle	0.79 RPM	0.52 RPM
SRP051959_spleen	0.78 RPM	0.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_648 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_648 has 0 orthologous retrocopies within eutheria group .

---

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,