RetrogeneDB ID: retro_hsap_448

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:146553889..146554501(-)
• Located in intron of: ENSG00000227242

Retrocopy information

• Ensembl ID: ENSG00000230832
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSB
• Ensembl ID: ENSG00000138385
• Aliases: SSB, LARP3, La, La/SSB
• Description: Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]

Sequence

>retro_hsap_448
GAAGCTAAATTAAGAGCTAAACAAGAGCAAGAAGCAAATCAAAAGTTAGAAGAAGATGCTGAAATGAAATCTCTAGAAGA
GAAGATTGGATGCTTGCTGAAGTTTTCAGGTGATTTAGATGATCAGACCTGTAGAGAAGATTTACACATCCTTTTCTCAA
GTCATGGTGAAATAAAATGGATAGACTTCATCAGAGGAGCAAAAGAGGGGATAATTCTATTTAAAGAAAAAGACAAGGAA
GCGTTGGGTAAAGCCAAAGATGTAAATAATGGTAATCTACAATTACAGAGCAAAGAAGTGACTTGGGAAGTACTAGAAGG
AGAGGTGGAAAGAGAAGCACTGAAAAAAATAACAGAAGACCAACAAGAATCCCTAAACATATGGAAGTCAAAAGGACACA
GATTTAAAGGAAAAGGAAAGGGTAATAAAGCTGCCCATCCTAGGTCTGGTAAAGAAAAAGTACAGTTTCAGGGCAAGAAA
ATGAAATTTGCTAATGATGATGAACATGATGAAAATGGTGCAACTGGACCTATGAAAAGATCAGGAGAAGAAACAGACAA
AGAAGAACCTGTGTCCAAACAACAGAAAAGAGAAAATGGTGCTGGAGACGAG

Alignment

ORF - retro_hsap_448 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAKLRAKQEQEAKQKLEEDAEMKSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEG
          EAKLRAKQEQEA.QKLEEDAEMKSLEEKIGCLLKFSGDLDDQTCREDLHILFS.HGEIKWIDF.RGAKEG
Retrocopy EAKLRAKQEQEANQKLEEDAEMKSLEEKIGCLLKFSGDLDDQTCREDLHILFSSHGEIKWIDFIRGAKEG

Parental  IILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKGRRFKGKGK
          IILFKEK.KEALGKAKD.NNGNLQL..KEVTWEVLEGEVE.EALKKI.EDQQESLN.WKSKG.RFKGKGK
Retrocopy IILFKEKDKEALGKAKDVNNGNLQLQSKEVTWEVLEGEVEREALKKITEDQQESLNIWKSKGHRFKGKGK

Parental  GNKAAQPGSGKGKVQFQGKKTKFASDDEHDEHDENGATGPVKRAREETDKEEPASKQQKTENGAGDQ
          GNKAA.P.SGK.KVQFQGKK.KFA.DDEHDE...NGATGP.KR..EETDKEEP.SKQQK.ENGAGD.
Retrocopy GNKAAHPRSGKEKVQFQGKKMKFANDDEHDE---NGATGPMKRSGEETDKEEPVSKQQKRENGAGDE

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
bodymap2_adipose	0.00 RPM	109.05 RPM
bodymap2_adrenal	0.00 RPM	92.13 RPM
bodymap2_brain	0.02 RPM	102.93 RPM
bodymap2_breast	0.00 RPM	115.97 RPM
bodymap2_colon	0.00 RPM	130.67 RPM
bodymap2_heart	0.00 RPM	46.21 RPM
bodymap2_kidney	0.00 RPM	105.62 RPM
bodymap2_liver	0.00 RPM	36.08 RPM
bodymap2_lung	0.00 RPM	63.31 RPM
bodymap2_lymph_node	0.00 RPM	81.61 RPM
bodymap2_ovary	0.00 RPM	131.53 RPM
bodymap2_prostate	0.00 RPM	104.56 RPM
bodymap2_skeletal_muscle	0.00 RPM	28.99 RPM
bodymap2_testis	0.06 RPM	111.76 RPM
bodymap2_thyroid	0.00 RPM	143.85 RPM
bodymap2_white_blood_cells	0.00 RPM	82.96 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_448 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	1:146555493..146556777
ENCFF002CMI	POLR2A	1:146555458..146557131
ENCFF002CSY	POLR2A	1:146555347..146556819

EST

No EST(s) were mapped for retro_hsap_448 retrocopy.

TSS

No TSS is located nearby retro_hsap_448 retrocopy 5' end.

Lab

retro_hsap_448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_448 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_433

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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,