RetrogeneDB ID: retro_ptro_1820

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:124133559..124134307(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSPTRG00000005240
• Aliases: None
• Description: None

Sequence

>retro_ptro_1820
TATGCTCTTCTCTATCAGCCTCTATTTGATAAGTGATTTGAGATTATTAATGCAATTTATGAACCTACAGAAGAAGAATG
TGAATAGATACCAGATGAAGATGGCAAGATTTCGGAGGAGTTGAAAGAAAAGGCCAAGATTGAAGAAGAGAAGAAGGATG
AAGAAAAAGAAGAGCCCATAGGAATTCCTGAATTTTGGTTAACTATTTTTAAGAATGTTGACTTGCTTAGTGATATGCTT
CAGGAACATGATGAACCTATTCTGAAGCACTTTAAATATATTAAAGTGAAGTTCTCGGTTGCTGGCCAGCCTATGAGTTT
TGTCTTAGAATTTCACTTTGAACCCAGTGAATATTTTACAAATGAAGTGCCAACAAAGACATATAAGATGAGGTCAGAAC
CAGATGATTCTGGTCCCTTTTCTTTTGATGGACTAGAAATTATGGGTTGTACAGGGTGCCAGATAGATTGGAAAAAAAGG
AAAGAATGTCACTTTGAGAAACATTAAGAAGCAGCAGAAACACAAGGGACATGGGACAGTTTGTACTGTGACTAAAAGAG
TTTCTAATGACTCTTGCTTTAATTTTTTTGCCCCTCCTGAAGTTCCTGAGAGTGGATATCTGGATGATGCTGCTGAAGCT
ATCCATGCTGCAAACTTCCAAATCAGTCACTTTTTACCTGAGCGTATAATCCCAAGATCAGTGTTATATTTTACTGGAGA
AGCTATTGAAGATGTTGATGATGATTAT

Alignment

ORF - retro_ptro_1820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.2 %
• Parental protein coverage: 63.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEEDEISEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVF
          YA.LYQPLFDK.FEIINAIYEPTEEECE..PDE...ISEE..................P.GIPEFWLT.F
Retrocopy YALLYQPLFDK*FEIINAIYEPTEEECE*IPDEDGKISEEXXXXXXXXXXXXXXXXXXPIGIPEFWLTIF

Parental  KNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPF
          KNVDLLSDM.QEHDEPILKH.K.IKVKFS.AGQPMSFVLEFHFEP.EYFTNEV.TKTY.MRSEPDDS.PF
Retrocopy KNVDLLSDMLQEHDEPILKHFKYIKVKFSVAGQPMSFVLEFHFEPSEYFTNEVPTKTYKMRSEPDDSGPF

Parental  SFDGPEIMGCTGCQIDW-KKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDD
          SFDG.EIMGCTGCQIDW.KKGKNVTL..IKK.QKHKG.GTV.TVTK.VSNDS.FNFFAPPEVPESG.LDD
Retrocopy SFDGLEIMGCTGCQIDW>KKGKNVTLRNIKKQQKHKGHGTVCTVTKRVSNDSCFNFFAPPEVPESGYLDD

Parental  DAEAILAADFEIGHFLRERIIPRSVLYFTGEAIEDDDDDY
          .AEAI.AA.F.I.HFL.ERIIPRSVLYFTGEAIED.DDDY
Retrocopy AAEAIHAANFQISHFLPERIIPRSVLYFTGEAIEDVDDDY

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	0.02 RPM	143.37 RPM
SRP007412_cerebellum	0.04 RPM	121.74 RPM
SRP007412_heart	0.03 RPM	171.58 RPM
SRP007412_kidney	0.00 RPM	92.66 RPM
SRP007412_liver	0.07 RPM	58.63 RPM
SRP007412_testis	0.00 RPM	219.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1820 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1820 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2696
Gorilla gorilla	retro_ggor_1879
Pongo abelii	retro_pabe_2287

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820 , retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,