RetrogeneDB ID: retro_hsap_2453

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:17459732..17460076(-)
• Located in intron of: ENSG00000125851

Retrocopy information

• Ensembl ID: ENSG00000232241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DYNLT3
• Ensembl ID: ENSG00000165169
• Aliases: DYNLT3, RP3, TCTE1L, TCTEX1L
• Description: dynein, light chain, Tctex-type 3 [Source:HGNC Symbol;Acc:11694]

Sequence

>retro_hsap_2453
ATGGAGGAGTACCATCGCCACTGCGACGAGGTTGGCCTCAATGCTGAGGAAGCCCACAATATTGTCAAAGAATGTGCAGA
CGGGGTTTTAGGTGGTGAAGATTATAATTACAACAACATCAACCAGTGGACCGCAAGCATAGTGGAATTATCGTTAACAC
ATCTGCCTAAGCTGGGAAAAGCTTATAAATGTATTGTGAAATGTGCAGTGGTCCAGAAGAGCGCATATGGCTTTCGCACA
GCAGCTCCTGTTTTTGGGATACCACATCTGATGGAACCTGTACCGTAAGATGGGAGAACTGGACCATGAACTGTATTGTC
AATGTTTTTGCCATTGCTGTTCTT

Alignment

ORF - retro_hsap_2453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEYHRHCDEVGFNAEEAHNIVKECVDGVLGGEDYNHNNINQWTASIVEQSLTHLVKLGKAYKYIVTCAV
          MEEYHRHCDEVG.NAEEAHNIVKEC.DGVLGGEDYN.NNINQWTASIVE.SLTHL.KLGKAYK.IV.CAV
Retrocopy MEEYHRHCDEVGLNAEEAHNIVKECADGVLGGEDYNYNNINQWTASIVELSLTHLPKLGKAYKCIVKCAV

Parental  VQKSAYGFHTA-SSCFWDTTSDGTCTVRWENRTMNCIVNVFAIAIV
          VQKSAYGF.TA.SSCFWDTTSDGTCTVRWEN.TMNCIVNVFAIA..
Retrocopy VQKSAYGFRTA<SSCFWDTTSDGTCTVRWENWTMNCIVNVFAIAVL

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	38.64 RPM
bodymap2_adrenal	0.00 RPM	33.45 RPM
bodymap2_brain	0.00 RPM	122.01 RPM
bodymap2_breast	0.00 RPM	48.62 RPM
bodymap2_colon	0.00 RPM	79.74 RPM
bodymap2_heart	0.00 RPM	24.11 RPM
bodymap2_kidney	0.00 RPM	93.33 RPM
bodymap2_liver	0.00 RPM	49.07 RPM
bodymap2_lung	0.00 RPM	119.41 RPM
bodymap2_lymph_node	0.00 RPM	41.85 RPM
bodymap2_ovary	0.00 RPM	50.22 RPM
bodymap2_prostate	0.00 RPM	69.83 RPM
bodymap2_skeletal_muscle	0.00 RPM	9.86 RPM
bodymap2_testis	0.00 RPM	58.71 RPM
bodymap2_thyroid	0.00 RPM	44.46 RPM
bodymap2_white_blood_cells	0.00 RPM	38.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2453 was not detected

EST

No EST(s) were mapped for retro_hsap_2453 retrocopy.

TSS

No TSS is located nearby retro_hsap_2453 retrocopy 5' end.

Lab

retro_hsap_2453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2453 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1417
Pongo abelii	retro_pabe_1804

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038156	1 retrocopy	retro_btau_907,
Canis familiaris	ENSCAFG00000013955	1 retrocopy	retro_cfam_1778,
Callithrix jacchus	ENSCJAG00000005227	1 retrocopy	retro_cjac_1247,
Cavia porcellus	ENSCPOG00000001932	1 retrocopy	retro_cpor_91,
Dasypus novemcinctus	ENSDNOG00000014826	1 retrocopy	retro_dnov_1638,
Felis catus	ENSFCAG00000026355	1 retrocopy	retro_fcat_1736,
Homo sapiens	ENSG00000146425	2 retrocopies	retro_hsap_1716, retro_hsap_2910,
Homo sapiens	ENSG00000165169	2 retrocopies	retro_hsap_2152, retro_hsap_2453 ,
Macropus eugenii	ENSMEUG00000013924	4 retrocopies	retro_meug_1294, retro_meug_1443, retro_meug_33, retro_meug_620,
Microcebus murinus	ENSMICG00000001440	1 retrocopy	retro_mmur_556,
Myotis lucifugus	ENSMLUG00000015093	1 retrocopy	retro_mluc_739,
Macaca mulatta	ENSMMUG00000013221	1 retrocopy	retro_mmul_660,
Monodelphis domestica	ENSMODG00000021109	7 retrocopies	retro_mdom_1023, retro_mdom_1145, retro_mdom_1432, retro_mdom_1745, retro_mdom_1748, retro_mdom_376, retro_mdom_935,
Mus musculus	ENSMUSG00000031176	1 retrocopy	retro_mmus_3147,
Nomascus leucogenys	ENSNLEG00000000985	2 retrocopies	retro_nleu_1900, retro_nleu_821,
Oryctolagus cuniculus	ENSOCUG00000009787	1 retrocopy	retro_ocun_836,
Pongo abelii	ENSPPYG00000020241	2 retrocopies	retro_pabe_1804, retro_pabe_2098,
Pan troglodytes	ENSPTRG00000021793	1 retrocopy	retro_ptro_1417,
Rattus norvegicus	ENSRNOG00000003611	2 retrocopies	retro_rnor_1462, retro_rnor_652,
Sarcophilus harrisii	ENSSHAG00000008069	2 retrocopies	retro_shar_141, retro_shar_825,
Tupaia belangeri	ENSTBEG00000014383	2 retrocopies	retro_tbel_3460, retro_tbel_885,
Vicugna pacos	ENSVPAG00000006367	1 retrocopy	retro_vpac_246,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).