RetrogeneDB ID: retro_ptro_2024

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:154050755..154051282(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK4
• Ensembl ID: ENSPTRG00000000827
• Aliases: None
• Description: None

Sequence

>retro_ptro_2024
AGCACAGAAGTTGGTGAGATGGCAAAGCAGTATATAGAGAAAAGTCTTTTCGTTCCAGACCATGTGATTACACACCTAAT
GATGTCTGAGTTGGAGAATAGGTGTGGCCAGCACTGGCTCCTCGATGGTTTTCCTAGGACATTAGGACAAGCCGAAGCCC
TGGACAAAATCTGTGAAGTGGATCTAGTGATCAGTTTGAACATTCCATTTGAAACACTTAAAGATCGTCTCAGCCGCCGT
TGGATTCACCCTCCTAGCAGAAGGGTATATAACCTGGACTTCAATCCACCTCATGTTCATGGTATTGATGTACTGGTGAA
CCATTAGTCCAGCAGGAGGATGATAAACCTGAAGCAGTTGCTGCCAGGCTAAGACAGTACAAAGACATGGCAAAGCCAGT
CATTGAATTATACAAAAGCTAAGGAGTGCTCCACCAATTTTCTGGGATGGAGACGAACAAAATCTGACCCTACATTTACA
CACTTTTCTCGAACAAGATCACACCTATTCAGTCCAAAGAAGCATAT

Alignment

ORF - retro_ptro_2024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 79.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STEVGEMAKQYIEKSLLVPDHVITRLMMSELENRRGQHWLLDGFPRTLGQAEALNKICEVDLVISLNIPF
          STEVGEMAKQYIEKSL.VPDHVIT.LMMSELENR.GQHWLLDGFPRTLGQAEAL.KICEVDLVISLNIPF
Retrocopy STEVGEMAKQYIEKSLFVPDHVITHLMMSELENRCGQHWLLDGFPRTLGQAEALDKICEVDLVISLNIPF

Parental  ETLKDRLSRRWIHPPSGRVYNLDFNPPHVHGIDDV-TGEPLVQQEDDKPEAVAARLRQYKDVAKPVIELY
          ETLKDRLSRRWIHPPS.RVYNLDFNPPHVHGI.DV.TGEPLVQQEDDKPEAVAARLRQYKD.AKPVIELY
Retrocopy ETLKDRLSRRWIHPPSRRVYNLDFNPPHVHGI-DV<TGEPLVQQEDDKPEAVAARLRQYKDMAKPVIELY

Parental  KSRGVLHQFSGTETNKIWPYVYTLFSNKITPIQSKEAY
          KS.GVLHQFSG.ETNKI.PY.YTLFSNKITPIQSKEAY
Retrocopy KS*GVLHQFSGMETNKI*PYIYTLFSNKITPIQSKEAY

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	5.79 RPM
SRP007412_cerebellum	0.04 RPM	23.30 RPM
SRP007412_heart	0.00 RPM	21.66 RPM
SRP007412_kidney	0.03 RPM	169.07 RPM
SRP007412_liver	0.00 RPM	20.95 RPM
SRP007412_testis	0.00 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2024 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2024 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2993
Gorilla gorilla	retro_ggor_2073
Pongo abelii	retro_pabe_2479

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Homo sapiens	ENSG00000162433	6 retrocopies	retro_hsap_1101, retro_hsap_1744, retro_hsap_2993, retro_hsap_3320, retro_hsap_3619, retro_hsap_4225,
Gorilla gorilla	ENSGGOG00000026644	4 retrocopies	retro_ggor_1301, retro_ggor_2073, retro_ggor_2444, retro_ggor_2829,
Myotis lucifugus	ENSMLUG00000009622	1 retrocopy	retro_mluc_1708,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,
Mus musculus	ENSMUSG00000028527	1 retrocopy	retro_mmus_1933,
Nomascus leucogenys	ENSNLEG00000015163	3 retrocopies	retro_nleu_1666, retro_nleu_2481, retro_nleu_743,
Otolemur garnettii	ENSOGAG00000016024	1 retrocopy	retro_ogar_3375,
Ochotona princeps	ENSOPRG00000010345	17 retrocopies	retro_opri_1094, retro_opri_153, retro_opri_291, retro_opri_328, retro_opri_357, retro_opri_417, retro_opri_438, retro_opri_442, retro_opri_666, retro_opri_724, retro_opri_73, retro_opri_743, retro_opri_752, retro_opri_765, retro_opri_889, retro_opri_892, retro_opri_947,
Pongo abelii	ENSPPYG00000001269	6 retrocopies	retro_pabe_1021, retro_pabe_2479, retro_pabe_2735, retro_pabe_2970, retro_pabe_3412, retro_pabe_3483,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024 , retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416, retro_ptro_796,