RetrogeneDB ID: retro_hsap_1533

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:21009041..21010134(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSG00000154639
• Aliases: CXADR, CAR, CAR4/6, HCAR
• Description: coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]

Sequence

>retro_hsap_1533
ATGGCGCTCCTGCTGCGCTTCGTGCTCCTGTGCAGAGTCGCGGATTTCATCAGAGGTTGGAGTATCACTACTCCTGAGCA
GATGATTGAAAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACGCTTAGTCCTGAAGACCAGGGACCACTGG
ACATCGAGTGGCTGATATCACCAGCTGATAATCAGAAGGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAATTTAT
GATGACTACTATCCAGATCTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
AACGAATTTTCAGCTGTCAGATATTGGCACAGATCAGTGCAAAGTGAAAAGAGCTCCTGGTGTTGCAAATAAGAAGATTC
AGCTGGTAGTTCTTGGTAAGCCTTCAGGTACAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAATTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTTC
ATGGTTAGCAGAAATGACTTCATCTGTTATATCTATAAAAATGCTTCTTCTGAGTACTCTGGGACATACAGCTGTACATC
AGAAACAGAGTGGGCTCTGATCAGTGCCTGTTGCGTGTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCAGG
AGCCATTATAGGAACTTTGCTTGCTCTAGTGCTCATTGGTCTTATCATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGAAA
AATATGAAAAGGAAGTTCATCACGATATCAAGGAAGATGTGCCGCCTCCAAAGAGCCGCACGTCCACTGCCAGAAGCTAC
ATAGGCAGTAATCATTCATCCCTGGGATCCATAACTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAAACAAGT
ACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCTAAGTCGAA
TGGGCGCGATTCCTGTGATGATTCCCGCACAGAGCAAGGATGGGTCTATAGTA

Alignment

ORF - retro_hsap_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLLCFVLLCGVVDFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
          MALLL.FVLLC.V.DF.R..SITTPE.MIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
Retrocopy MALLLRFVLLCRVADFIRGWSITTPEQMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV

Parental  IILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
          IILYSGDKIYDDYYPDLKGRVHF.SNDLKSGDASINVTN.QLSDIGT.QCKVK.APGVANKKI.LVVL.K
Retrocopy IILYSGDKIYDDYYPDLKGRVHFKSNDLKSGDASINVTNFQLSDIGTDQCKVKRAPGVANKKIQLVVLGK

Parental  PSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV-KNASSEYSGT
          PSG.RCYVDGSEEIGSDFK.KCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVIS..KNASSEYSGT
Retrocopy PSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISI<KNASSEYSGT

Parental  YSCT-VRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIR
          YSCT..RNRVGSDQCLLR.NVVPPSNKAGLIAGAIIGTLLAL.LIGLIIFCCRKKRREEKYEKEVHHDI.
Retrocopy YSCT<IRNRVGSDQCLLRVNVVPPSNKAGLIAGAIIGTLLALVLIGLIIFCCRKKRREEKYEKEVHHDIK

Parental  EDVPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSRM
          EDVPPPKSRTSTARSYIGSNHSSLGS..PSNMEGYSKTQY.QVPSEDFERTPQSPTLPPAKVAAPNLSRM
Retrocopy EDVPPPKSRTSTARSYIGSNHSSLGSITPSNMEGYSKTQYKQVPSEDFERTPQSPTLPPAKVAAPNLSRM

Parental  GAIPVMIPAQSKDGSIV
          GAIPVMIPAQSKDGSIV
Retrocopy GAIPVMIPAQSKDGSIV

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
bodymap2_adipose	0.00 RPM	0.74 RPM
bodymap2_adrenal	0.00 RPM	23.70 RPM
bodymap2_brain	0.00 RPM	57.03 RPM
bodymap2_breast	0.00 RPM	14.14 RPM
bodymap2_colon	0.00 RPM	16.67 RPM
bodymap2_heart	0.00 RPM	32.93 RPM
bodymap2_kidney	0.00 RPM	43.47 RPM
bodymap2_liver	0.00 RPM	31.35 RPM
bodymap2_lung	0.00 RPM	21.96 RPM
bodymap2_lymph_node	0.00 RPM	5.24 RPM
bodymap2_ovary	0.00 RPM	14.65 RPM
bodymap2_prostate	0.00 RPM	62.23 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	1.87 RPM	53.18 RPM
bodymap2_thyroid	0.00 RPM	45.63 RPM
bodymap2_white_blood_cells	0.00 RPM	0.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1533 was not detected

EST

No EST(s) were mapped for retro_hsap_1533 retrocopy.

TSS

No TSS is located nearby retro_hsap_1533 retrocopy 5' end.

Lab

retro_hsap_1533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1533 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
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
Pongo abelii	retro_pabe_1273

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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,