RetrogeneDB ID: retro_ptro_1612

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:75579635..75580652(-)
• Located in intron of: ENSPTRG00000012101

Retrocopy information

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

Parental gene information

• Parental gene symbol: AUH
• Ensembl ID: ENSPTRG00000021099
• Aliases: None
• Description: None

Sequence

>retro_ptro_1612
ATGGCGGCCGCGGTGGCGGCGGCACCTGGGGCCTTGGGATCCCTGCATGCTGGCGGCGCCCGCCTGGTGGCCGCTTGCAG
TGCGTGGCTCTGCCCGGGGTTGAGGCTGCCCGGCTCGTTGGCAGGCCGGCGAGTGGGCCCGGCGATCTGGGCCCAGGGCT
GGGTACCTGCGGCCGGGGGTCCCGCCCCGAAAAGGGGCTACAGCTCTGAGGTGAAGACGGAGGACGAGCTGCGGGTGCGG
CACCTGGAGGAGGAGAACCGAGGAATTGTGGTGCTTGGAATAAACAGAGCTTATGGCAAAAATTCACTCAGTAAAAATCT
TATAAAAATGCTATCAAAAGCTGTGGATGCTTTGAAATCTGATAAGAAAGTACGGACCATAATAATCAGGAGTGAAGTCC
CAGGGATATTCTGTGCTGGTGCTGACCTTAAGGAAAGAGCCAAAATGAGTTCCAGTGAAGTTGGTCTTTTTGTCTCCAAA
GTAAGAGCAGTGATTAACGATATTGCTAATCTTCCAGTACCAACAATTGCAGCAATAGATGGACTCGTTTTAGGTGGTGG
TCTTGAACTGGCTTTAGCCTGTGATATACGAGTAGCAGCTTCCTCTGCAAAAATGGGCCTGGTTGAAACAAAATTGGCGA
TTATTCCTGGTGGAGGGGGGACACAGCGATTGCCACGCGCCATTGGAATGTCCCTGGCCAAGGAGCTCATATTCTCTGCG
CGAGTCCTCGATGGCCAAGAAGCCAAAGCAGTGGGCTTAATCAGCCACGTTCTGGAACAGAACCAGGAGGGAGACGCGGC
CTACAGAAAGGCCTTGGACCTGGCGAGAGAGTTTTTACCTCAGGGACCTGTTGCAATGAGAGTGGCAAAATTAGCAATTA
ATCAAGGGATGGAGGTCGATTTAGTAACAGGGTTAGCCATAGAAGAAGCTTGTTATGCTCAGACCATTCCAACAAAAGAC
AGACTTGAAGGTCTTCTTGCTTTTAAAGAGAAAAGGCCCCCTCGCTATAAAGGAGAA

Alignment

ORF - retro_ptro_1612 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVAAAPGALGSLHAGGARLVAACSAWLCPGLRLPGSLAGRRVGPAIWAQGWVPAAGGPAPKRGYSSE
          MAAAVAAAPGALGSLHAGGARLVAACSAWLCPGLRLPGSLAGRRVGPAIWAQGWVPAAGGPAPKRGYSSE
Retrocopy MAAAVAAAPGALGSLHAGGARLVAACSAWLCPGLRLPGSLAGRRVGPAIWAQGWVPAAGGPAPKRGYSSE

Parental  VKTEDELRVRHLEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAG
          VKTEDELRVRHLEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAG
Retrocopy VKTEDELRVRHLEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAG

Parental  ADLKERAKMSSSEVGPFVSKIRAVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAKMGLVET
          ADLKERAKMSSSEVG.FVSK.RAVINDIANLPVPTIAAIDGL.LGGGLELALACDIRVAASSAKMGLVET
Retrocopy ADLKERAKMSSSEVGLFVSKVRAVINDIANLPVPTIAAIDGLVLGGGLELALACDIRVAASSAKMGLVET

Parental  KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP
          KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP
Retrocopy KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP

Parental  QGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE
          QGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE
Retrocopy QGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE

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
SRP007412_brain_prefrontal_cortex	0.48 RPM	8.76 RPM
SRP007412_cerebellum	0.00 RPM	7.49 RPM
SRP007412_heart	0.17 RPM	4.20 RPM
SRP007412_kidney	0.05 RPM	8.81 RPM
SRP007412_liver	0.00 RPM	2.49 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1612 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005695	1 retrocopy	retro_cjac_93,
Cavia porcellus	ENSCPOG00000001066	1 retrocopy	retro_cpor_503,
Oreochromis niloticus	ENSONIG00000011227	1 retrocopy	retro_onil_68,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090,
Pan troglodytes	ENSPTRG00000021099	1 retrocopy	retro_ptro_1612 ,