RetrogeneDB ID: retro_pabe_1273

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:18562253..18563348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSPPYG00000011295
• Aliases: None
• Description: coxsackievirus and adenovirus receptor homolog precursor [Source:RefSeq peptide;Acc:NP_001127547]

Sequence

>retro_pabe_1273
ATGGCGCTCTTGCTGCGCTTCGTGCTCCTGTGCGGAGTCGCGGATTTCACCGGAAGTTTGAGTATCACTGCTCCTGAGCA
GATGACTGAGAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACACTTAGTGCCGAAGACCAGGGGCCACTGG
ACATCGAGTGGCTGATATCACCAGCAGATAATCAGAACGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTAT
GATGACTACTACCCAGATCTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
AACGAATTTACAGCTGTCAGATACTGGCACAGATCAGTGTAAAGTGAAAAAAGCTCCTGGTGTTGCAAATAAGAAGATTT
AGCTGGTAGTTCTTGTTAAGCCTTCAGGTACAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAACTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACACAAAATGCCCACTTC
GTGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAAATGCTTCTTCTGCGTACTCTGGGACATACAGCTGTACAG
TCAGAAACAGAGTGGGCTCTGATCAGTGCCTGTTGTGTGTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCA
GGAGCCATTATAGAAACTTTGCTTGCTCTAGTGCTCATTGGTCTTATCATCTTTTGCTGTCGTGAAAAGCGCAGAGAAGA
AAAATATGAAAAGGAAGTTCATCACGATATCAGGGAAGATGTGCCGCCTCCAAAGAGCCGTACGTCCACCGCCAGAAGCT
ACATAGGCAGTAATCATTCATCCCTGGGATCCATGTCTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAAACAA
GTACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCCAAGTCG
AATGGGCGCGATTCCTGTGATGATTCTGGCACAGAGCAAGGATGGGTCTACAGTA

Alignment

ORF - retro_pabe_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLLRFVLLCGVADFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
          MALLLRFVLLCGVADF..SLSIT.PE.M.EKAKGETAYLPCKFTLS.EDQGPLDIEWLISPADNQ.VDQV
Retrocopy MALLLRFVLLCGVADFTGSLSITAPEQMTEKAKGETAYLPCKFTLSAEDQGPLDIEWLISPADNQNVDQV

Parental  IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
          IILYSGDKIYDDYYPDLKGRVHF.SNDLKSGDASINVTNLQLSD.GT.QCKVKKAPGVANKKI.LVVLVK
Retrocopy IILYSGDKIYDDYYPDLKGRVHFKSNDLKSGDASINVTNLQLSDTGTDQCKVKKAPGVANKKI*LVVLVK

Parental  PSGARCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTLWLAEMTSSVISVKNASSEYSGTY
          PSG.RCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDS.KMPT.WLAEMTSSVISVKNASS.YSGTY
Retrocopy PSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSHKMPTSWLAEMTSSVISVKNASSAYSGTY

Parental  SCTVRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIRED
          SCTVRNRVGSDQCLL..NVVPPSNKAGLIAGAII.TLLAL.LIGLIIFCCR.KRREEKYEKEVHHDIRED
Retrocopy SCTVRNRVGSDQCLLCVNVVPPSNKAGLIAGAIIETLLALVLIGLIIFCCREKRREEKYEKEVHHDIRED

Parental  VPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSRMGA
          VPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQY.QVPSEDFERTPQSPTLPPAKVAAPN.SRMGA
Retrocopy VPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYKQVPSEDFERTPQSPTLPPAKVAAPNPSRMGA

Parental  IPVMIPAQSKDGSIV
          IPVMI.AQSKDGS.V
Retrocopy IPVMILAQSKDGSTV

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	0.06 RPM	5.31 RPM
SRP007412_cerebellum	0.00 RPM	4.01 RPM
SRP007412_heart	0.00 RPM	17.16 RPM
SRP007412_kidney	0.00 RPM	6.86 RPM
SRP007412_liver	0.00 RPM	11.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1273 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1273 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1533
Homo sapiens	retro_hsap_1535
Pan troglodytes	retro_ptro_995
Pan troglodytes	retro_ptro_801
Homo sapiens	retro_hsap_1918
Pan troglodytes	retro_ptro_1244
Pan troglodytes	retro_ptro_1444

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012975	1 retrocopy	retro_dnov_990,
Homo sapiens	ENSG00000154639	6 retrocopies	retro_hsap_1533, retro_hsap_1535, retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys	ENSNLEG00000002063	2 retrocopies	retro_nleu_138, retro_nleu_58,
Pongo abelii	ENSPPYG00000011295	2 retrocopies	retro_pabe_1273 , retro_pabe_2776,
Pan troglodytes	ENSPTRG00000013795	4 retrocopies	retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995,
Sarcophilus harrisii	ENSSHAG00000005309	1 retrocopy	retro_shar_252,