RetrogeneDB ID: retro_ptro_2509

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:11084455..11085061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSB
• Ensembl ID: ENSPTRG00000012620
• Aliases: None
• Description: None

Sequence

>retro_ptro_2509
GTGGAAGCTAAATTAAGAGCTAAACAAGAGCAAGAAGCAAAACAAAAGAAGATGCTGAAATGAAATCTCTAGAAGAAAAG
ATTGGATGCTTGCTGAAATTTTTGGGTGATTTAGATGATCAGACCTGTAAAGAAGATTTACACATCCTTTTCTCAAATCA
TGGTGAAATAAAATGCTCCTTCATCAGAGGAGCAAAAGAGGGGATAATTCTATTTAAAGAAAAAGCCAAGGAAACATTGG
GTAAAGCCAAAGATGCAAATAATGGTAACCTACAATTAAGGAGCAAAGAAGTGACTTGGGAAGTACTAGAAGGAGAGCTG
GAAAAAGAAGTACTGAAAAAAATAACAGAAGACCAACAAGAATCCCTAAACAAATGGAAGTCAAAAGGTTGCAGATTTAA
AGGAAAAAGAAAGGGTAATAAAGCTGCCCAGCCTGGGTCTGGTAAAGGAAAAGTACAATTTCAGGACAAGAAAACAAAGT
TTGCTAGTGATGACGCACATGATGAAAATGGTTCAACTGGACCTATGAAAAAGAGGAAGAGAAGAAACAGACAAAGAATA
ACCTGCATCCAAACAACCGAAAACAGAAAATGGTGCTGGAGACCAG

Alignment

ORF - retro_ptro_2509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEAKLRAKQEQE-AKQKLEEDAEMKSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK
          VEAKLRAK..QE.A..K..EDAEMKSLEEKIGCLLKF.GDLDDQTC.EDLHILFSNHGEIK...F.RGAK
Retrocopy VEAKLRAK--QE<ARSKTKEDAEMKSLEEKIGCLLKFLGDLDDQTCKEDLHILFSNHGEIK-CSFIRGAK

Parental  EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKGRRFKGK
          EGIILFKEKAKE.LGKAKDANNGNLQLR.KEVTWEVLEGE.EKE.LKKI.EDQQESLNKWKSKG.RFKGK
Retrocopy EGIILFKEKAKETLGKAKDANNGNLQLRSKEVTWEVLEGELEKEVLKKITEDQQESLNKWKSKGCRFKGK

Parental  GKGNKAAQPGSGKGKVQFQGKKTKFASDDEHDEHDENGATGPV-KRAREETDKEEPASKQQKTENGAGDQ
          .KGNKAAQPGSGKGKVQFQ.KKTKFASDD.HDE...NG.TGP..KR.REETDKE.PASKQ.KTENGAGDQ
Retrocopy RKGNKAAQPGSGKGKVQFQDKKTKFASDDAHDE---NGSTGPM>KRGREETDKE*PASKQPKTENGAGDQ

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	36.62 RPM
SRP007412_cerebellum	0.07 RPM	59.01 RPM
SRP007412_heart	0.03 RPM	49.87 RPM
SRP007412_kidney	0.03 RPM	45.71 RPM
SRP007412_liver	0.00 RPM	39.51 RPM
SRP007412_testis	6.43 RPM	64.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2509 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2509 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509 ,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,