RetrogeneDB ID: retro_cjac_2806

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:45997247..45998640(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007506
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STK38
• Ensembl ID: ENSCJAG00000016045
• Aliases: None
• Description: None

Sequence

>retro_cjac_2806
ATGGCAATGACAGGCTCAACACCTTGCTCATCCATGAGTAACCACACAAAGGAAAGGGTGACAATGACCAAAGTGACACT
GGAGAATTTTTATAGCAACCTTATCGCTCAAAATGAAGAACGAGAAATGAGACAAAAGAAATTAGAAAAGGTGATGGAAG
AAGAAGGCCTAAAAGATGAGGAGAAATGACTCAGAAGATCAGCACATGCTCGGAAGGAAACGGTTTCTTCCTTTGAAGAG
AACAAGACTTGGATTGGAAGATTTTGAGTCCTTAAAAGTCATAGGTAGAGGAGCATTTGGTGAGGTACAGCTTGTTCAGA
AGAAAGATACAGGGCATGTGTATGCAATGAAAATACTCCGTAAAGCAGATATGCTTGAAAAAGAGCAGGTTGGCCACATT
CGTGCGGAGTGTGACATTCTAGTGGAGGCAGACAGTTTGTGGGTTGTGAAAATGTTCTATAGTTTTCAGGATAAGCTAAA
CCTCTACCTAATCATGGAGTTCCTGCCTGGAGGGGACATGATGACCTTGTTGATGAAAAAAGACACTCTGACAGAAGAAG
AGACTCAGTTTTATATAGCAGAAACAGTATTAGCCATAGACTCTATTCACCAACTTGGATTCATCCACAGAGACATCAAA
CCAGACAACCTTCTTTTGGACAGCAAGGGCCATGTGAAACTTTCTGACTTTGGTCTTTGCACAGGACTGAAAAAAGCACA
CAGGACAGAATTTTATAGGAATCTGAACCACAGCCTCCCCAGTGATTTCACATTCCAGAACATGAATTCCAAAAGGAAAG
CAGAAACCTGGAAAAGAAATAGACGTCAGCTAGCCTTCTCCACAGTAGGCACTCCTGACTACATTGCTCCTGAGGTGTTC
ATGCAGACCGGGTACAACAAGCTCTGTGATTGGTGGTTGCTTGGGGTGATCACGTATGAGATGCTCATCGGCTACCCACC
TTTCTGTTCTGAGACCCCTCAAGAGACATATAAGAAGGTGATGAACTGGAAAGAAACTTTGACTTTTCCTCCAGAAGTTC
CCATCTCTGAGAAAGCCAAGGATCTAATTTTGAGATTCTGCTGTGAATGGGAACATAGAATTGGAGCTCCTGGAGTTGAG
GAAATCAAAAGTAACTCTTTTTTTGAAGGTGTTGACTGGGAACATATCAGAGAGAGACCTGCTGCAATATCTATTGAAAT
CAAAAGCATTGATGATACCTCAAACTTCTATGAGTTTCCAGAGTCTGATATTCTTAAGCCAACAGTGGCCACAAGTAATC
ACCCTGAGACTGATTACAAGAACAAAGACTGGGTCTTCATCAATTACACATACAAGCACTTTGAGGGTCTGACTGCAAGT
GGGGCAATACCTTCCTACAGGAATGCAGCAAAA

Alignment

ORF - retro_cjac_2806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMTGSTPCSSMSNHTKERVTMTKVTLENFYSNLIAQHEEREMRQKKLEKVMEEEGLKDEEKRLRRSA-H
          MAMTGSTPCSSMSNHTKERVTMTKVTLENFYSNLIAQ.EEREMRQKKLEKVMEEEGLK..E....R...H
Retrocopy MAMTGSTPCSSMSNHTKERVTMTKVTLENFYSNLIAQNEEREMRQKKLEKVMEEEGLK-DEEK*LRRS>H

Parental  ARKETEFLRLKRTRLGLEDFESLKVIGRGAFGEVRLVQKKDTGHVYAMKILRKADMLEKEQVGHIRAERD
          ......FL.LKRTRLGLEDFESLKVIGRGAFGEV.LVQKKDTGHVYAMKILRKADMLEKEQVGHIRAE.D
Retrocopy MLGRKRFLPLKRTRLGLEDFESLKVIGRGAFGEVQLVQKKDTGHVYAMKILRKADMLEKEQVGHIRAECD

Parental  ILVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFI
          ILVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFI
Retrocopy ILVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFI

Parental  HRDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAETWKRNRRQLA
          HRDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAETWKRNRRQLA
Retrocopy HRDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAETWKRNRRQLA

Parental  FSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIAGYPPFCSETPQETYKKVMNWKETLTFPPEVP
          FSTVGTPDYIAPEVFMQTGYNKLCDWW.LGVI.YEMLI.GYPPFCSETPQETYKKVMNWKETLTFPPEVP
Retrocopy FSTVGTPDYIAPEVFMQTGYNKLCDWWLLGVITYEMLI-GYPPFCSETPQETYKKVMNWKETLTFPPEVP

Parental  ISEKAKDLILRFCCEWEHRIGAPGVEEIKSNSFFEGVDWEHIRERPAAISIEIKSIDDTSNFDEFPESDI
          ISEKAKDLILRFCCEWEHRIGAPGVEEIKSNSFFEGVDWEHIRERPAAISIEIKSIDDTSNF.EFPESDI
Retrocopy ISEKAKDLILRFCCEWEHRIGAPGVEEIKSNSFFEGVDWEHIRERPAAISIEIKSIDDTSNFYEFPESDI

Parental  LKPTVATSNHPETDYKNKDWVFINYTYKRFEGLTARGAIPSYMKAAK
          LKPTVATSNHPETDYKNKDWVFINYTYK.FEGLTA.GAIPSY..AAK
Retrocopy LKPTVATSNHPETDYKNKDWVFINYTYKHFEGLTASGAIPSYRNAAK

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	0.16 RPM	30.02 RPM
SRP051959_heart	0.19 RPM	15.03 RPM
SRP051959_kidney	0.22 RPM	18.50 RPM
SRP051959_liver	0.15 RPM	9.34 RPM
SRP051959_lung	0.21 RPM	34.26 RPM
SRP051959_lymph_node	0.71 RPM	42.94 RPM
SRP051959_skeletal_muscle	0.15 RPM	11.55 RPM
SRP051959_spleen	0.23 RPM	28.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2806 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2806 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011126	1 retrocopy	retro_btau_389,
Callithrix jacchus	ENSCJAG00000016045	2 retrocopies	retro_cjac_2806 , retro_cjac_2824,
Tarsius syrichta	ENSTSYG00000012409	2 retrocopies	retro_tsyr_1276, retro_tsyr_1603,