RetrogeneDB ID: retro_pabe_3679

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:99954261..99955207(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSGALNACT2
• Ensembl ID: ENSPPYG00000002209
• Aliases: None
• Description: chondroitin sulfate N-acetylgalactosaminyltransferase 2 [Source:HGNC Symbol;Acc:24292]

Sequence

>retro_pabe_3679
GATAAGGGCATGCAGTATGAACTCTTTTTTAAGAAAGCAGATTTTATGGAATATAGACATGTGACCCTCTTCTGCCCTTT
TGGACCTCTCATGAAAGTGAAGAGCGAGATGATTGACATCATCAGATCAATTATTATTAATATCATTATGCCACTTGCTG
AAAGAACTGAAGCACTTGTACAGTTTATGCAGAACTTCAGGGAGGTTTGTATTCATCAAGACAAGATTCATCTCACAGTG
GTGTATTTTGGTAACGAAGGACTGTCTAAAGTCAAGTCTAGCCTAGAATCTGTCACAAGTGAGTCTAATTTTTCACAATT
ACACCGTGGTCTCATTGAATGAAGAATTTAATCATGGATGAGGACTAAATGTGGGTGCCCAAGCTTGGGACAAGGGAGAG
GTCTTTATGTTTTTCTGTGATGTTGATATCTATTTCTCAGCCGAATTCCTTAACAGCTGACAGTTAAATGCTGAGCCTGG
TAAGAAAGTGTTTTACCCTGTGGTGTTCAGTCTTTACAATCCTTCCATTGTTTATGCCAACCAGGAAGTGCCATCACCTG
TGGAGCAGCAGCTGGTTCACAAAAAGGATTCTGGCTTTTGGAGAGATTTTGGCTTTGGAATGACTTGTCAGTATCGATCT
GATTTCCTGATCATTGGTGGATTTGACATGGAAGTGAAAGGTTGGGGTGGAGAAGATGTTCATCTTTATCAAAAATACTT
ACATGGTGACCTCATTGTGATTTGGACTCCGATTCCTGGTCTTTTCCACCTCTGGCCTGAAAAACGCTGTGCTGATGAGC
TGACCCCTGAGCAGTACCGCATGTGCATCCAGTCTAAAGCCATAATTGAGGCCTCTCACTCCCACCTGAGAATGCTGGTA
TTCAGGGAGGAAATAGAGACGTATCTTCATAAACAGGCATACAGGACAAACAGCAAAGCTGTTGGT

Alignment

ORF - retro_pabe_3679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKGTQYELFFKKADLMEYRHVTLFRPFGPLMKVKSEMIDITRSII-NIIVPLAERTEAFVQFMQNFRDVC
          DKG.QYELFFKKAD.MEYRHVTLF.PFGPLMKVKSEMIDI.RSII.NII.PLAERTEA.VQFMQNFR.VC
Retrocopy DKGMQYELFFKKADFMEYRHVTLFCPFGPLMKVKSEMIDIIRSIIINIIMPLAERTEALVQFMQNFREVC

Parental  IHQDKKIHLTVVYFGKEGLSKVKSVLESVTSESNF-HNYTLVSLNEEFNRGRGLNVGARAWDKGEVLMFF
          IHQDK.IHLTVVYFG.EGLSKVKS.LESVTSESNF.HNYT.VSLNEEFN.G.GLNVGA.AWDKGEV.MFF
Retrocopy IHQDK-IHLTVVYFGNEGLSKVKSSLESVTSESNF>HNYTVVSLNEEFNHG*GLNVGAQAWDKGEVFMFF

Parental  CDVDIYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIVYANQEVPPPVEQQLVHKKDSGFWRDFGFGMT
          CDVDIYFSAEFLNS..LNAEPGKKVFYPVVFSLYNP.IVYANQEVP.PVEQQLVHKKDSGFWRDFGFGMT
Retrocopy CDVDIYFSAEFLNS*QLNAEPGKKVFYPVVFSLYNPSIVYANQEVPSPVEQQLVHKKDSGFWRDFGFGMT

Parental  CQYRSDFLTIGGFDMEVKGWGGEDVHLYRKYLHGDLIVIRTPVPGLFHLWHEKRCADELTPEQYRMCIQS
          CQYRSDFL.IGGFDMEVKGWGGEDVHLY.KYLHGDLIVI.TP.PGLFHLW.EKRCADELTPEQYRMCIQS
Retrocopy CQYRSDFLIIGGFDMEVKGWGGEDVHLYQKYLHGDLIVIWTPIPGLFHLWPEKRCADELTPEQYRMCIQS

Parental  KAMNEASHSHLGMLVFREEIETHLHKQAYRTNSEAVG
          KA..EASHSHL.MLVFREEIET.LHKQAYRTNS.AVG
Retrocopy KAIIEASHSHLRMLVFREEIETYLHKQAYRTNSKAVG

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	0.00 RPM	16.37 RPM
SRP007412_cerebellum	0.00 RPM	23.71 RPM
SRP007412_heart	0.00 RPM	8.88 RPM
SRP007412_kidney	0.03 RPM	10.94 RPM
SRP007412_liver	0.03 RPM	13.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3679 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3679 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4732

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169826	1 retrocopy	retro_hsap_4732,
Pongo abelii	ENSPPYG00000002209	1 retrocopy	retro_pabe_3679 ,
Tupaia belangeri	ENSTBEG00000012462	2 retrocopies	retro_tbel_2719, retro_tbel_4730,