RetrogeneDB ID: retro_pabe_2776

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:124997510..124998603(-)
• 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_2776
GTGGCCCTCCTGCTGCGCTTCGTGCTCCTGTGCGGAGTAGCGGATTTTGCCAGAAGTTTGAGTATCACTACTCCTGAAGA
GATGATTGAAAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACGCTTAGTCCCGAAGACCAGGGACCGCTGG
ACATCGAGTGGCTGATATCACCAGCGGATAATCAGAACGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTAT
GACGACTACTATCCAGATCTGAAAGGCCGAGTACATTTTACGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
AACGAATTTACAGCTGTCAGATATTGGCACATATCAGTGCAAAGTGAAAAAAGCTCCTGGTGTTGCAAATAAGAAGATTC
ATCTGGTAGGTCTTGTTAAGCCTTCAGGTGCAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAACTA
AAATATGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTTT
GTGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAAATGCCTCTTCTGAGTACTCCGGGACATACAGCTGTACAG
TCAGAAACAGAGTGGGCTCTGCTCAGTGCCTGTTGCGTCTAAACTTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCA
GGAGCCATTATAGGAACTTTGCTTGCTCTGGCGCTCATTGGTCTTATCATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGA
AAAATATGAAAAGGAAATTCATCACGATATCAGGGAAGATGTGCCATCTCCAAAGAGCCGTACGTCCACTGCCAGAAGCT
ACATCGGCAGTAATCATTCATCCCTGGGATCCATGTCTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAACCAA
CTACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCGCTAAGGTAGCTGCCCCTAATCTAAGTCGA
ATGGGCGCGATTCCTGGATGATTCCAGCACAGAGCAAGGATGGGTCTATAGTA

Alignment

ORF - retro_pabe_2776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLLRFVLLCGVADFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
          .ALLLRFVLLCGVADFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQ.VDQV
Retrocopy VALLLRFVLLCGVADFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQNVDQV

Parental  IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
          IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLV.LVK
Retrocopy IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVGLVK

Parental  PSGARCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTLWLAEMTSSVISVKNASSEYSGTY
          PSGARCYVDGSEEIGSDFKLK.EPKEGSLPLQYEWQKLSDSQKMPTLWLAEMTSSVISVKNASSEYSGTY
Retrocopy PSGARCYVDGSEEIGSDFKLKYEPKEGSLPLQYEWQKLSDSQKMPTLWLAEMTSSVISVKNASSEYSGTY

Parental  SCTVRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIRED
          SCTVRNRVGS.QCLLRLN.VPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKE.HHDIRED
Retrocopy SCTVRNRVGSAQCLLRLNFVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEIHHDIRED

Parental  VPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPP-AKVAAPNLSRMG
          VP.PKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQ.PSEDFERTPQSPTLPP.AKVAAPNLSRMG
Retrocopy VPSPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQLPSEDFERTPQSPTLPP<AKVAAPNLSRMG

Parental  AIP-VMIPAQSKDGSIV
          AIP..MIPAQSKDGSIV
Retrocopy AIP<WMIPAQSKDGSIV

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_2776 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2776 has 0 orthologous retrocopies within eutheria group .

---

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,