RetrogeneDB ID: retro_pabe_3408

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:49344215..49345083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSB
• Ensembl ID: ENSPPYG00000012919
• Aliases: None
• Description: Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]

Sequence

>retro_pabe_3408
TCTATTTATATCAAAGGCTTCCCAACTGTTGCAACTATTGATGACATAAAAGAATGATTAGAACATAGAGGTCAAGTACA
AAATATACCAATGAGAAGAACATTGCATAAAACATTTAAAGGATCAGTGTTTGCTGTGTTTGATAACATTAAATCTGCTA
AAAAGTTTGTAGAGACCCCTGGCCAGAAGTACAAAGACACAGCCTACTAATACTTTTCAAGGAATATCACTTTGCTGAAA
AAAGTGAAGAAAGGAGACAAAATAATATGGAGAATAAATTAAGAGCTAAACAAGAGCAAGAAGAAAAATAAAAGCTACAT
GATGCTGAAATGAAATCTCTAGAGAAAAGATTGGATGCTTGCTGAAATTTTTGGGTGACTTAGATGATCAGACCTGTAGA
GAAGGTTCACACATCCTTTTCTCAAATCATGGTGAACTAAAATGGATAGACGTTGTCAGAGGTGCAAAAGGGAATAATTC
GATTTAAAGAAAAAGTCGAGGAAGCATTGGGTAAAGCCAAAGATGCAAATAATGGTAATCTACAATTAAGGAACAAAGAA
GTGACTTGGGAAGTACTAGAAGGACAGGTGGAAAAAGAAGCATTGAAAAAATCATAAAAGACCAACACGAACCCCAAACA
AATGGAAGTCAAAAGGTCGCAGATTTAAAAGGAAAGGGTAATAAAGCGGCCTCGCCTGAGTTTGTTAAAGGAAAGGTACA
GCTTCAGGGCAAGAAAATGAAATTTGTTAGTGATGATGAACATGATGAAAATGGTGCAACTGGACCAGTGAAAAGAGCAA
GAGAAGAAACAGACAAAAAAGAATCTGCATCAAAACAACAGAAAACAGAAAATGATGCTAGAGACCAA

Alignment

ORF - retro_pabe_3408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 72.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKET-DL
          S.YIKGFPT.AT.DDIKE.LE..GQV.NI.MRRTLHK.FKGS.F.VFD.I.SAKKFVETPGQKYK.T..L
Retrocopy SIYIKGFPTVATIDDIKE*LEHRGQVQNIPMRRTLHKTFKGSVFAVFDNIKSAKKFVETPGQKYKDT<SL

Parental  LILFKDDYFAKKNEERKQNKVEAKLRAKQEQEAKQKLEEDAEMKSLE-EKIGCLLKFSGDLDDQTCREDL
          LILFK...FA.K.EER.QN..E.KLRAKQEQE.K.KL..DAEMKSLE.EKIGCLLKF.GDLDDQTCRE..
Retrocopy LILFKEYHFAEKSEERRQNNMENKLRAKQEQEEK*KL-HDAEMKSLE<EKIGCLLKFLGDLDDQTCREGS

Parental  HILFSNHGEIKWIDFVRGAKEGIIL-FKEKAKE-ALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALK-
          HILFSNHGE.KWID.VRGAK.......K.K....ALGKAKDANNGNLQLRNKEVTWEVLEG.VEKEALK.
Retrocopy HILFSNHGELKWIDVVRGAKGNNSI<LKKKSRK<ALGKAKDANNGNLQLRNKEVTWEVLEGQVEKEALK<

Parental  KIIEDQQE-SLNKWKSKGRRF-KGKGKGNKAAQPGSGKGKVQFQGKKTKFASDDEHDENGATGPVKRARE
          KII.DQ.E...NKWKSKGRRF.KGKG..........GK...Q..GKK.KF.SDDEHDENGATGPVKRARE
Retrocopy KIIKDQHE<TPNKWKSKGRRF>KGKGNKAASPEFVKGKVQLQ--GKKMKFVSDDEHDENGATGPVKRARE

Parental  ETDKEEPASKQQKTENGAGDQ
          ETDK.E.ASKQQKTEN.A.DQ
Retrocopy ETDKKESASKQQKTENDARDQ

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	0.17 RPM	35.33 RPM
SRP007412_cerebellum	0.00 RPM	25.78 RPM
SRP007412_heart	0.03 RPM	15.77 RPM
SRP007412_kidney	0.03 RPM	27.51 RPM
SRP007412_liver	0.00 RPM	17.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3408 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3408 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1153

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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,