RetrogeneDB ID: retro_ptro_819

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:47468618..47469672(+)
• 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_819
ATGGCAGACATTGACAACAAAGAACAGTCTGAACTTGATCAAGATTTGGATGACGCTGAAAAAGTAGAAGAAGGAACTGG
TGAAGAAACAGAAATCAAAGCACATCAGCTAACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAGAAA
GACTTGATGGTCTAATAGAAACACCAACAGGATACATTGAAAGCCTGCCTAGGGTAGTTAAAAAAACAAGTGAATGCTCT
CAAACACCTGTAAGTTAAATGTGCACAGACAGAAGCCAAATTCAATGAGGAAGTTCACAATCTTGAAAGGAAGTATGCTG
TTCTCTGTCAGCCTCTATTTGATAAGCAATTTGAGATTATTAATGCAATTACGAACCTACAGAAGAAGAATGGAAACCAG
ATGAAGAAGATGAGATCTCAGAGGAGTTGAAAGAAAAGGCCATGATTGAAGATGAGAAAAAAGATGAAGAAAAAAAAGAT
TCCAAAGGAATTCCTGAATTTCGGTTAACTGTTTTTAAGAATGTTGACTTGCTCAGTGATATGCTTCAGGAGCATGATGA
ACCTATTCTGAAGCACTTGAAAGATATTAAAGTGAAGTTCTCAGATGCTTGCCAGCCCATGAGTTTTGTCTTAGAATTTC
ACTTTGAAGACAATGAATATTTTACAAATGAAGTGCTGACAAAGACGTATAGCATGAGGTCAGAACCAGATGATTCTGAT
CCCTTTTATTTTGATGGACCAGAAATTATGGGTTTTACAGGGTGCCAGATAGATTGGAAAAAAGGAAAGAATGTCACTTT
GAAAACCATTAAGAAGAAGCAGAAACACAAGGGACGTGGGACAGTTAGTACTGTGACTAAAACAGTTTCCAATGACTCTT
TCTTTAAATTTTTTGCCCCTCCTGAAGTTTCTGAGAGCGGAGATCGGGATGATGATGCTAAAACAATCCTTGCTGCAGAC
TTCGAAACTGGTCACTTTTTACCTGAACATATAATCTCAGGATCAGTGTTATACTTTACTGGAGAAGCTATTGAAGATGG
ATGATGATGATTAT

Alignment

ORF - retro_ptro_819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 90.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKEQSELDQDLDDVEEVEEEETGEETKLKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADIDNKEQSELDQDLDD.E.VEE..TGEET..KA.QLTVQMMQNPQILAALQERLDGL.ETPTGYIESL
Retrocopy MADIDNKEQSELDQDLDDAEKVEEG-TGEETEIKAHQLTVQMMQNPQILAALQERLDGLIETPTGYIESL

Parental  PRVVKR-RVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAI-YEPTEEECEWKPDE
          PRVVK...VNALK.L.VKCAQ.EAKF.EEVH.LERKYAVL.QPLFDK.FEIINAI.YEPTEEE..WKPDE
Retrocopy PRVVKK>QVNALKHL*VKCAQTEAKFNEEVHNLERKYAVLCQPLFDKQFEIINAI<YEPTEEE--WKPDE

Parental  EDEISEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQ
          EDEISEE.................D.KGIPEF.LTVFKNVDLLSDM.QEHDEPILKHLKDIKVKFSDA.Q
Retrocopy EDEISEEXXXXXXXXXXXXXXXXXDSKGIPEFRLTVFKNVDLLSDMLQEHDEPILKHLKDIKVKFSDACQ

Parental  PMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQK
          PMSFVLEFHFE.NEYFTNEVLTKTY.MRSEPDDSDPF.FDGPEIMG.TGCQIDWKKGKNVTLKTIKKKQK
Retrocopy PMSFVLEFHFEDNEYFTNEVLTKTYSMRSEPDDSDPFYFDGPEIMGFTGCQIDWKKGKNVTLKTIKKKQK

Parental  HKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEAIE
          HKGRGTV.TVTKTVSNDSFF.FFAPPEV.ESGD.DDDA..ILAADFE.GHFL.E.II..SVLYFTGEAIE
Retrocopy HKGRGTVSTVTKTVSNDSFFKFFAPPEVSESGDRDDDAKTILAADFETGHFLPEHIISGSVLYFTGEAIE

Parental  D-DDDDY
          D.DDDDY
Retrocopy D>DDDDY

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	0.04 RPM	143.37 RPM
SRP007412_cerebellum	0.04 RPM	121.74 RPM
SRP007412_heart	0.09 RPM	171.58 RPM
SRP007412_kidney	0.03 RPM	92.66 RPM
SRP007412_liver	0.00 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_819 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_819 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1199
Gorilla gorilla	retro_ggor_934

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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,