RetrogeneDB ID: retro_hsap_4159

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:38478814..38479344(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000215165
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSG00000187735
• Aliases: TCEA1, GTF2S, SII, TCEA, TF2S, TFIIS
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_hsap_4159
GAGATATTTGTTTCATCTGTTCCTCGGCACGAAGCGCTTCTAATTCTGTGCGGATGAAGTACAGGGAGATGCTTGCTGCA
GCTCTTCGAACAGGAGATGACTGCATTGAAATGGGAGCTGATGAGGAAGAATTAGGATCTCGAATTGAGGAAGCTGTAGA
TCCAGAAAGAGGGAATACAGGCATGAAGTACAAAAATAGAGTCCAAAGTAAGATATCAAATCTTACAGATGCAAAGAATC
CAAATTTAAGGAAAAATGCATCGTGTGGGAATATTCCTCCTGACTTACTTGCTAGAATGTCCGCAGAAGAAATGGCTAGC
GATGAGCTCAAAGAGATGCACAAAAACTTGACGAAAGAAGCCATCAGAGAGCATCAGATGGCCAAGACAGGTGGAACCCA
GCCTGATTCGCTCACATGTGGCAAATGTAAAAAGAATTGCACTTCCACACAGGTACAAGCCTGCAGTGTTGGTGAACCAA
TGGCAACGTTTGTTGACTGTAATGAATGTGGAAATCAACAGAAGTTCTGT

Alignment

ORF - retro_hsap_4159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.09 %
• Parental protein coverage: 63.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTYVSSFPR-APSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVR
          ...VSS.PR.A.S.S.SVR.K.REMLAAALRTGDD.I..GADEEELGS.IEEA...E..NT.MKYKNRV.
Retrocopy EIFVSSVPR<ARSASNSVRMKYREMLAAALRTGDDCIEMGADEEELGSRIEEAVDPERGNTGMKYKNRVQ

Parental  SRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFT
          S.ISNL.DAKNPNLRKN..CGNIPPDL.ARM.AEEMASDELKEM.KNLTKEAIREHQMAKTGGTQ.D..T
Retrocopy SKISNLTDAKNPNLRKNASCGNIPPDLLARMSAEEMASDELKEMHKNLTKEAIREHQMAKTGGTQPDSLT

Parental  CGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC
          CGKC.KKNCT.TQVQ..S..EPM.TFV.CNECGN..KFC
Retrocopy CGKC-KKNCTSTQVQACSVGEPMATFVDCNECGNQQKFC

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	81.32 RPM
bodymap2_adrenal	0.00 RPM	81.04 RPM
bodymap2_brain	0.02 RPM	60.99 RPM
bodymap2_breast	0.00 RPM	80.55 RPM
bodymap2_colon	0.00 RPM	101.17 RPM
bodymap2_heart	0.00 RPM	31.18 RPM
bodymap2_kidney	0.00 RPM	61.61 RPM
bodymap2_liver	0.00 RPM	41.17 RPM
bodymap2_lung	0.00 RPM	55.47 RPM
bodymap2_lymph_node	0.00 RPM	69.71 RPM
bodymap2_ovary	0.00 RPM	97.04 RPM
bodymap2_prostate	0.00 RPM	108.44 RPM
bodymap2_skeletal_muscle	0.00 RPM	64.33 RPM
bodymap2_testis	0.30 RPM	86.48 RPM
bodymap2_thyroid	0.00 RPM	108.83 RPM
bodymap2_white_blood_cells	0.00 RPM	84.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4159 was not detected

EST

No EST(s) were mapped for retro_hsap_4159 retrocopy.

TSS

No TSS is located nearby retro_hsap_4159 retrocopy 5' end.

Lab

retro_hsap_4159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4159 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2794

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159 , retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 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	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.07 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).