RetrogeneDB ID: retro_cjac_2824

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:85150269..85151663(-)
• Located in intron of: ENSCJAG00000011557

Retrocopy information

• Ensembl ID: ENSCJAG00000011570
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2824
ATGGCAATGACAGGCTCAACACCTTGCTCATCCATAAGTAACCACGCAAAAGAAAGGGTGACAATGACCAAAGTGACACT
GGAGAACTTTTACAGCAACCTTATCACTCAACATGAAGAACGAGAAATGAGACAAAAGAAGTTAGAAAAGGTGAAGGAAG
AAGAAGCTGTAAAAGATGAGGAGAAAAGACTCAGAAGATCAGCACATTTTCAGAAGGAAACAGAGTTTCATCGTTTGAAG
AGAACAAGACTTGGATTGGAAGATTTTGAGTCCTTAAAAGTAATAGGCAGAGGAGCATTTGGTGAGGTATGGCTTGTTCA
GAAGAAAGATACGGGGCATGTGTATGCAACGAAAATACTCTGTAAAGCAGATATGCTTGAAAAAGAGCAGGTTGGCCACA
TTCGTGTGGAGCATAACATTCTAGTGGAGGCAGACAGTTTGTGGGTTGTGAAAATGTTCTATAGTTTTCAGGATAAGCTA
AACCTCTACCTAATCATGGAGTTCCTGCCTGGAGGGGACATGATGACCTTGTTGATGAAAAAAGACACTCTGACAGAAGA
AGAGACTCAGTTTTATATAGCAGAAACAGTATCAGCCATAGACTCTATCCACCAACTTGGATTCATCCACAGAGACATCA
AACCAGACAACCTTCTTTTGGACAGCAAGGGCCATGTGAAACTTTCTGACTTCGGTCTTTGCACAGGACTGAAAAAAGCA
CACAGGACAGAATTTTATAGGAATCTGAACCACAGCCTCCCCAGTGATTTCACTTTCCAGAACATGAATTCCAAAAGGAA
AGCAGAAATCTGGAAAAGAAATAGACGTCAGCTAGCCTTCTCCACAGTAGGCACTCCTGACTACATTGCTTCTGAGGTGT
TCATGCAGACCAGATACAACAAGCTCTGTGACTGGTGGTTGCTTGGGGTAATCATGTATGAGATGCTCATCGGCTACCCA
CCTTTCTGTGCTGAGACCCCTCAAGAGACATATAAGAAGGTGATGAACTGGAAAGAAACTTTGACTTTTCCTCCAGAAGT
TCCCATCCCTGAAAAAGCCAAGGATCTAATTTTGAGATGCTGCTGTGAATGGGAGCATAGAATTGCAGCTCCTGGAGTTG
AGGAAATCAAAAGTAACTCTTTTTTTGAAGGCGTTGACTGGGAACATATCAGAGTGAGACCAGCTGCAATATCTATTGAA
ATCAAAAGCATTGATGATACCTCAAACTTCAATGAGTTTCCAGAATCTGATATTCTTAAGCCAACAGTGGCCACAAGTAA
TCACCCTGAGACTGACTAAAGAACAAAGACTGGGTCTTCATCAATTACACATACAAGCGCTTTGAGGGTCTGACTGAAAG
TGGGGCAATACCTTCCTACAGGAAAGCAGCAAAA

Alignment

ORF - retro_cjac_2824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMTGSTPCSSMSNHTKERVTMTKVTLENFYSNLIAQHEEREMRQKKLEKVMEEEGLKDEEKRLRRSAHA
          MAMTGSTPCSS.SNH.KERVTMTKVTLENFYSNLI.QHEEREMRQKKLEKV.EEE..KDEEKRLRRSAH.
Retrocopy MAMTGSTPCSSISNHAKERVTMTKVTLENFYSNLITQHEEREMRQKKLEKVKEEEAVKDEEKRLRRSAHF

Parental  RKETEFLRLKRTRLGLEDFESLKVIGRGAFGEVRLVQKKDTGHVYAMKILRKADMLEKEQVGHIRAERDI
          .KETEF.RLKRTRLGLEDFESLKVIGRGAFGEV.LVQKKDTGHVYA.KIL.KADMLEKEQVGHIR.E..I
Retrocopy QKETEFHRLKRTRLGLEDFESLKVIGRGAFGEVWLVQKKDTGHVYATKILCKADMLEKEQVGHIRVEHNI

Parental  LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFIH
          LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETV.AIDSIHQLGFIH
Retrocopy LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVSAIDSIHQLGFIH

Parental  RDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAETWKRNRRQLAF
          RDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAE.WKRNRRQLAF
Retrocopy RDIKPDNLLLDSKGHVKLSDFGLCTGLKKAHRTEFYRNLNHSLPSDFTFQNMNSKRKAEIWKRNRRQLAF

Parental  STVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIAGYPPFCSETPQETYKKVMNWKETLTFPPEVPI
          STVGTPDYIA.EVFMQT.YNKLCDWW.LGVIMYEMLI.GYPPFC.ETPQETYKKVMNWKETLTFPPEVPI
Retrocopy STVGTPDYIASEVFMQTRYNKLCDWWLLGVIMYEMLI-GYPPFCAETPQETYKKVMNWKETLTFPPEVPI

Parental  SEKAKDLILRFCCEWEHRIGAPGVEEIKSNSFFEGVDWEHIRERPAAISIEIKSIDDTSNFDEFPESDIL
          .EKAKDLILR.CCEWEHRI.APGVEEIKSNSFFEGVDWEHIR.RPAAISIEIKSIDDTSNF.EFPESDIL
Retrocopy PEKAKDLILRCCCEWEHRIAAPGVEEIKSNSFFEGVDWEHIRVRPAAISIEIKSIDDTSNFNEFPESDIL

Parental  KPTVATSNHPETD-YKNKDWVFINYTYKRFEGLTARGAIPSYMKAAK
          KPTVATSNHPETD..KNKDWVFINYTYKRFEGLT..GAIPSY.KAAK
Retrocopy KPTVATSNHPETD<LKNKDWVFINYTYKRFEGLTESGAIPSYRKAAK

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	0.09 RPM	30.02 RPM
SRP051959_heart	0.00 RPM	15.03 RPM
SRP051959_kidney	13.22 RPM	18.50 RPM
SRP051959_liver	5.07 RPM	9.34 RPM
SRP051959_lung	0.05 RPM	34.26 RPM
SRP051959_lymph_node	0.02 RPM	42.94 RPM
SRP051959_skeletal_muscle	0.04 RPM	11.55 RPM
SRP051959_spleen	0.06 RPM	28.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2824 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2824 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,