RetrogeneDB ID: retro_ptro_2514

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:27798740..27799324(+)
• Located in intron of: ENSPTRG00000019030

Retrocopy information

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

Parental gene information

• Parental gene symbol: NANOG
• Ensembl ID: ENSPTRG00000029807
• Aliases: None
• Description: Pan troglodytes Nanog homeobox (NANOG), mRNA. [Source:RefSeq mRNA;Acc:NM_001071827]

Sequence

>retro_ptro_2514
ATGAGTGTGGATCTGGCTTGTCTGCAAAGCTTGCCTTGCTTCGAAGCATCCGACTGTAAAGAATCTTCACCTATGGCTGT
GATTTGTGGGCCTGAAGAAAACTATCCATCTTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGTCTCTCCTC
TTCTTCCTCCGTGGATCTGCTTATTCAGGACAGCCCTGATTCTTCCACCAGTCCCAAAGGCAAACAACCCATTGCTGCAG
AGAATAGGGCCCCAAAAAAGGGAGACAAGGTCCCAGTCAAGAAACAGAAGACCAGAACTCTGTTTTCTTCCACCCAGCTG
TGTGTACTCAATGATAGATTTCAGAGACAGAAATACCTCAGCCTCCAGCAGATGCAAGAACTCTCAAATATCTGGAACCT
CAGCTACAAACAGGTGAAGACCTGGTTCTAGAACCAGAGAATGAAATCTAAGAGGTGGCAGAAAAACAACTGGCCGAAGA
ATAGCAATGGTGTGACTCGGAAGGCCTCAGCACCTACCTACCCCAGCCACTACTCTTCCTACCACCAGGGATGACTGGTG
AACCTGACTGGGAACCTTCCAATG

Alignment

ORF - retro_ptro_2514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.31 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVDPACPQSLPCFEASDCKESSPMPVICGPEENYPSLQMSSAEMPHTETVSPL-PSSMDLLIQDSPDSS
          MSVD.AC.QSLPCFEASDCKESSPM.VICGPEENYPSLQMSSAEMPHTETVSPL..SS.DLLIQDSPDSS
Retrocopy MSVDLACLQSLPCFEASDCKESSPMAVICGPEENYPSLQMSSAEMPHTETVSPL<SSSVDLLIQDSPDSS

Parental  TSPKGKQPTSAENSVTKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV
          TSPKGKQP..AEN...KK.DKVPVKKQKTRT.FSSTQLCVLNDRFQRQKYLSLQQMQELSNI.NLSYKQV
Retrocopy TSPKGKQPIAAENRAPKKGDKVPVKKQKTRTLFSSTQLCVLNDRFQRQKYLSLQQMQELSNIWNLSYKQV

Parental  KTWFQNQRMKSKRWQKNNWPKNSNGVTQKASAPTYPSLYSSYHQGCLVNPTGNLPM
          KTWF.NQRMKSKRWQKNNWPKNSNGVT.KASAPTYPS.YSSYHQG.LVN.TGNLPM
Retrocopy KTWF*NQRMKSKRWQKNNWPKNSNGVTRKASAPTYPSHYSSYHQG*LVNLTGNLPM

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	0.04 RPM
SRP007412_cerebellum	0.32 RPM	0.04 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2514 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2514 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3713
Gorilla gorilla	retro_ggor_2510
Pongo abelii	retro_pabe_3142

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017064	1 retrocopy	retro_amel_354,
Canis familiaris	ENSCAFG00000013914	1 retrocopy	retro_cfam_724,
Choloepus hoffmanni	ENSCHOG00000000972	4 retrocopies	retro_chof_1267, retro_chof_264, retro_chof_794, retro_chof_987,
Cavia porcellus	ENSCPOG00000002621	1 retrocopy	retro_cpor_1132,
Echinops telfairi	ENSETEG00000004648	8 retrocopies	retro_etel_1155, retro_etel_1334, retro_etel_134, retro_etel_1434, retro_etel_1935, retro_etel_630, retro_etel_818, retro_etel_963,
Felis catus	ENSFCAG00000001621	1 retrocopy	retro_fcat_932,
Homo sapiens	ENSG00000111704	5 retrocopies	retro_hsap_1455, retro_hsap_1549, retro_hsap_3713, retro_hsap_4814, retro_hsap_722,
Gorilla gorilla	ENSGGOG00000028196	4 retrocopies	retro_ggor_1812, retro_ggor_2510, retro_ggor_3000, retro_ggor_608,
Macropus eugenii	ENSMEUG00000009949	2 retrocopies	retro_meug_266, retro_meug_940,
Microcebus murinus	ENSMICG00000002228	1 retrocopy	retro_mmur_575,
Myotis lucifugus	ENSMLUG00000029325	2 retrocopies	retro_mluc_1562, retro_mluc_2054,
Myotis lucifugus	ENSMLUG00000030580	1 retrocopy	retro_mluc_169,
Macaca mulatta	ENSMMUG00000032158	4 retrocopies	retro_mmul_1901, retro_mmul_2466, retro_mmul_964, retro_mmul_979,
Monodelphis domestica	ENSMODG00000017979	2 retrocopies	retro_mdom_1293, retro_mdom_1938,
Mustela putorius furo	ENSMPUG00000016731	5 retrocopies	retro_mputfur_1140, retro_mputfur_1553, retro_mputfur_261, retro_mputfur_553, retro_mputfur_691,
Nomascus leucogenys	ENSNLEG00000005359	3 retrocopies	retro_nleu_1086, retro_nleu_2189, retro_nleu_2340,
Oryctolagus cuniculus	ENSOCUG00000013783	1 retrocopy	retro_ocun_971,
Otolemur garnettii	ENSOGAG00000026339	1 retrocopy	retro_ogar_568,
Procavia capensis	ENSPCAG00000015460	2 retrocopies	retro_pcap_143, retro_pcap_429,
Pongo abelii	ENSPPYG00000004233	5 retrocopies	retro_pabe_2157, retro_pabe_3142, retro_pabe_3440, retro_pabe_3742, retro_pabe_623,
Pan troglodytes	ENSPTRG00000029807	4 retrocopies	retro_ptro_1746, retro_ptro_2514 , retro_ptro_3203, retro_ptro_990,
Pteropus vampyrus	ENSPVAG00000006989	1 retrocopy	retro_pvam_1251,