RetrogeneDB ID: retro_hsap_3384

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:126512391..126512726(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000271585
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SELT
• Ensembl ID: ENSG00000198843
• Aliases: None
• Description: selenoprotein T precursor [Source:RefSeq peptide;Acc:NP_057359]

Sequence

>retro_hsap_3384
ATTAAGATGAGGCTTCTGCTACTTCTCCTGGTGGTGTCGGCAGTGGTGGCCAACCTGGGCAGCATGCCCAGCAAGAGATT
AAAGATGCAATACACCACAGGGCCACCGCTCAAGTTCTAGATTTCTGTTTCCTAAGGTTACAGGTGGGTGTTTGAGGAGC
ACATGTGGGTTATTAGCCAGCAGTACCCAGACATCACACTGAAGGAGAGAATTACCTCCCTCAACCAATATATAGACACA
TAGCATCTTTCCTGACAGCCTTCAGTCTATTACTAATAGGGTTAATAATTGTTGTCAAGGATCCTTTTGCTTTCTTTGGC
ATACAAGCTCCTAGC

Alignment

ORF - retro_hsap_3384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.94 %
• Parental protein coverage: 59.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLLLLLLVAASAMVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIR
          ....LLLL......V.S...ANLG..PSKRLKMQY.TGP.LKF.I.VS.GYR.VFEE.M.VISQ.YPDI.
Retrocopy IKMRLLLLL----LVVSAVVANLGSMPSKRLKMQYTTGPPLKF*ISVS*GYRWVFEEHMWVISQQYPDIT

Parental  I-EGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPS
          ..EGENYLPQPIYRHIASFL..F.L.LIGLIIV.KDPFAFFG.QAPS
Retrocopy L<EGENYLPQPIYRHIASFLTAFSLLLIGLIIVVKDPFAFFGIQAPS

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	48.20 RPM
bodymap2_adrenal	0.00 RPM	86.83 RPM
bodymap2_brain	0.00 RPM	152.97 RPM
bodymap2_breast	0.00 RPM	82.32 RPM
bodymap2_colon	0.00 RPM	83.28 RPM
bodymap2_heart	0.00 RPM	61.72 RPM
bodymap2_kidney	0.00 RPM	143.09 RPM
bodymap2_liver	0.00 RPM	64.64 RPM
bodymap2_lung	0.00 RPM	90.14 RPM
bodymap2_lymph_node	0.00 RPM	114.06 RPM
bodymap2_ovary	0.00 RPM	91.04 RPM
bodymap2_prostate	0.00 RPM	94.50 RPM
bodymap2_skeletal_muscle	0.00 RPM	38.16 RPM
bodymap2_testis	0.00 RPM	94.93 RPM
bodymap2_thyroid	0.00 RPM	88.83 RPM
bodymap2_white_blood_cells	0.00 RPM	148.31 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3384 was not detected

EST

No EST(s) were mapped for retro_hsap_3384 retrocopy.

TSS

No TSS is located nearby retro_hsap_3384 retrocopy 5' end.

Lab

retro_hsap_3384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384 , retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,