RetrogeneDB ID: retro_ptro_2211

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:175561355..175562352(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAPDHS
• Ensembl ID: ENSPTRG00000010848
• Aliases: GAPDHS, GAPDS
• Description: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Source:HGNC Symbol;Acc:24864]

Sequence

>retro_ptro_2211
AAGGTGAAGGCTGCAGTCAATGGATTTGGTTGTACTGAACACCTGGTCACCAAGGCTGCTTTTAACTCTGGTAAAGTGGA
TATTGTCACCATCAATGACCCCTTCATTGACCTCAACTCCATGGTCTACATGTTCCAGTATGATTCCACCCATGGCAAAT
TCTGTGGCACCGTCAAGGCTGAGAACAGGAAGCTTGTCACCAGTGGAAATCCCATCACCATCTTCCAGGGCGAGATCCCT
CCAAAATCAAATGGGGTGATGCTGGTGCTCAGTACATTGTGGAGTCTACTTGTATCTTCACCACCATGGAGAAGGCTGGG
GCTCACTTGCAGGGAGGAGCCAAAAGGGTCATCATCTCTGCCCCCTCTGCTGATGCCCCCATGTTCGTGATGGATGTGAA
CCACGAGAAGTATGACAACAGCCTCAAGATCGTCAGCAATGCCTCCTGCATCACCAACTGCTTAGCGCCCCTGGCCAACG
TCATCCACAACTTTGGTATCGTGGAAGGACCCATGACCACAGTCCATGCTATCACTGCCACCCAGAAGATTGTGGATGGC
CTCTCCGGGAAACTGGCATAACGGCCATGGAGCTCTCCAGAACATCATCCCTGCCTCTACTGGCACTGCCAAAGCTGTGG
GCAAGGTCATCCCTGAGTTGAACAGGAAGCTCACTGGCATGGGATTCTGTGTCCTCACTGCCAATGTGTTGGTCATGGAC
CCGACATGCCATCTGGAAAAACCTACCAAATACAATGACATCAAGAAGGTGGTAAAGCAGGCATCCAACGCCCCCTCAAG
GGCATCCTGGGCTACACGAGCACCAGGTGGTCTCCTCCGACTTCAACAGCGACACCCACACCCACTCTTCCACCTTCAAT
GCTGGGGCTGGCACTGCCCTCGATGGTCACTTTGTCAAGCTCATTTCCTGGTATGACAATGCATTTGGCTACAGCAACAG
GGTGGTGAACCTCAGGGCCCACATGGCCGCCAAGGAG

Alignment

ORF - retro_ptro_2211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.84 %
• Parental protein coverage: 81.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ELTVGINGFGRIGRLVLRACMEKG-VKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNH
          ......NGFG....LV..A....G.V..V..NDPFID...MVYMF.YDSTHG...G.V...N..LV....
Retrocopy KVKAAVNGFGCTEHLVTKAAFNSGKVDIVTINDPFIDLNSMVYMFQYDSTHGKFCGTVKAENRKLVTSGN

Parental  EISVYQC-KEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPTFVMGVNENDYN
          .I...Q....P..I.W...G..Y.VEST........A..H...GA.RV.ISAPS.DAP.FVM.VN...Y.
Retrocopy PITIFQG<RDPSKIKWGDAGAQYIVESTCIFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMDVNHEKYD

Parental  PGSMNIVSNASCTTNCLAPLAKVIHEQFGIVEGLMTTIHSYTATQKTVDG-PSRKA-WRDGRGAHQNIIP
          ..S..IVSNASC.TNCLAPLA.VIH..FGIVEG.MTT.H..TATQK.VDG.P.R...W..G.GA.QNIIP
Retrocopy -NSLKIVSNASCITNCLAPLANVIHN-FGIVEGPMTTVHAITATQKIVDG<PLRET<WHNGHGALQNIIP

Parental  ASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKG-PMAGILAYT
          ASTG.AKAV.KVIPEL..KLTGM.F.V.T..V.V.D.TC.L..P..Y..IK..VK.A....P..GIL.YT
Retrocopy ASTGTAKAVGKVIPELNRKLTGMGFCVLTANVLVMDPTCHLEKPTKYNDIKKVVKQASNA<PLKGILGYT

Parental  -EDEVVSMDFLGD--THSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRD
          .E..VVS.DF..D..THSS.F.A.AG.AL...FVKLISWYDN..GYS.RVV.L...M....
Retrocopy <EHQVVSSDFNSDTHTHSSTFNAGAGTALDGHFVKLISWYDNAFGYSNRVVNLRAHMAAKE

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	0.25 RPM	2.54 RPM
SRP007412_cerebellum	0.18 RPM	4.34 RPM
SRP007412_heart	0.03 RPM	0.93 RPM
SRP007412_kidney	0.00 RPM	3.03 RPM
SRP007412_liver	0.00 RPM	1.54 RPM
SRP007412_testis	0.00 RPM	280.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2211 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2211 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3268
Gorilla gorilla	retro_ggor_2224
Pongo abelii	retro_pabe_2706
Macaca mulatta	retro_mmul_2056

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000061099	2 retrocopies	retro_mmus_3024, retro_mmus_528,
Otolemur garnettii	ENSOGAG00000009491	25 retrocopies	retro_ogar_1269, retro_ogar_1332, retro_ogar_1460, retro_ogar_1472, retro_ogar_1798, retro_ogar_1968, retro_ogar_2074, retro_ogar_2266, retro_ogar_2376, retro_ogar_2446, retro_ogar_2469, retro_ogar_2631, retro_ogar_2647, retro_ogar_2884, retro_ogar_2957, retro_ogar_315, retro_ogar_3197, retro_ogar_3262, retro_ogar_3517, retro_ogar_355, retro_ogar_468, retro_ogar_582, retro_ogar_632, retro_ogar_658, retro_ogar_785,
Petromyzon marinus	ENSPMAG00000009321	1 retrocopy	retro_pmar_9,
Pan troglodytes	ENSPTRG00000004577	43 retrocopies	retro_ptro_1008, retro_ptro_1009, retro_ptro_1065, retro_ptro_1133, retro_ptro_1337, retro_ptro_1390, retro_ptro_1513, retro_ptro_1539, retro_ptro_1573, retro_ptro_173, retro_ptro_1832, retro_ptro_1847, retro_ptro_186, retro_ptro_187, retro_ptro_188, retro_ptro_189, retro_ptro_190, retro_ptro_191, retro_ptro_1932, retro_ptro_2001, retro_ptro_2092, retro_ptro_2309, retro_ptro_2365, retro_ptro_2409, retro_ptro_2447, retro_ptro_2459, retro_ptro_248, retro_ptro_2487, retro_ptro_2506, retro_ptro_2777, retro_ptro_285, retro_ptro_2939, retro_ptro_2986, retro_ptro_3196, retro_ptro_3209, retro_ptro_322, retro_ptro_3310, retro_ptro_369, retro_ptro_507, retro_ptro_661, retro_ptro_748, retro_ptro_811, retro_ptro_815,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211 ,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346,