RetrogeneDB ID: retro_hsap_3843

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:46039222..46040377(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000221971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSG00000243725
• Aliases: None
• Description: tetratricopeptide repeat domain 4 [Source:HGNC Symbol;Acc:12394]

Sequence

>retro_hsap_3843
ATGGAGTAACCTGAGCAGGACCCCACCTCAGACGATGCCACGGACTTGTTCCTGGAAAAGTTCCAGAGCCAGCCTTACCG
TGGCGGCTTTCATGAGGACCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGCGCCATCAGAAATTG
ATCCCAGGGAGAATCCTGACTTGGCTTGTCTCCAGTCAATTATTTTTGATGGGGAGCATTCTCCAGAACAGGCCAAGACC
TATAAAGATGAGGGCAATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAGGGATTAAAGAA
GAAATGTGCAAATCCTGATTTGAGTGCTGTCCTTTATACCAACCGGGCAGCAGCACAATACTATCTGGGCAATTTTCATT
CTGCTCTCCGTGATGTGACAGCTGCCAAAAAGTTAAAACCGTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCAT
CTGGAACTGAAACACTTTGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCT
GGAAATGAGGGCTAAAGTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGA
GGAATCAGAATGAAGTTTTACTCCAGGATACCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTT
TCAGCCTCAGAAGGTCTAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGA
TGACCAGGGCAGGCTGAGCTGGCCTGTGCTCTTTCTGTACCCAGAGTATGCCCAATCGGATTTCATCTCTGCTTTTCATG
AGGACTCCAGATTTATTGATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCT
GATAATTTGGAGGTCTATATTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCACCTTGCTGCAGGA
TCTACAGCACCACAGGCACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTGTGTAGGATCCAAACTTTTTTGAAAGA
ATTATCTCTGGGGGAGAAAGGTGCACCAGGTAAGA

Alignment

ORF - retro_hsap_3843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEQPGQDPTSDDVMDSFLEKFQSQPYRGGFHEDQWEKEFEKVPLFMSRAPSEIDPRENPDLACLQSIIFD
          ME.P.QDPTSDD..D.FLEKFQSQPYRGGFHEDQWE.EFEKVPLFM..APSEIDPRENPDLACLQSIIFD
Retrocopy ME*PEQDPTSDDATDLFLEKFQSQPYRGGFHEDQWEEEFEKVPLFMKKAPSEIDPRENPDLACLQSIIFD

Parental  EERSPEEQAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDV
          .E.SPE.QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCA.PDL.AVLYTNRAAAQYYLGNF.SAL.DV
Retrocopy GEHSPE-QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCANPDLSAVLYTNRAAAQYYLGNFHSALRDV

Parental  TAARKLKPCHLKAIIRGALCHLELKHFAEAVNWCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANL
          TAA.KLKPC.LKAIIRGALCHLELKHFA.AVN.CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANL
Retrocopy TAAKKLKPCYLKAIIRGALCHLELKHFAKAVN*CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANL

Parental  KEKKERNQNEALLQAIKARNIRLSEAACEDEDSASEGLGELFLDGLSTENPHGARLSLDGQGRLSWPVLF
          KEK.ERNQNE.LLQ..KARNIRLSEAACEDE.SASEGLGELFLDGLS.ENPHGARLSLD.QGRLSWPVLF
Retrocopy KEK-ERNQNEVLLQDTKARNIRLSEAACEDEVSASEGLGELFLDGLSSENPHGARLSLDDQGRLSWPVLF

Parental  LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVL
          LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVY.EDEDRAELY.VPAKSTLLQ.L
Retrocopy LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYIEDEDRAELYWVPAKSTLLQDL

Parental  QHQRYFVKALTPAFLVCVGSSPFCKNFLRGRKVYQIR
          QH.R.FVKALTPAFLVCVGS..F.KN.L.GRKV.Q.R
Retrocopy QHHRHFVKALTPAFLVCVGSKLF*KNYLWGRKVHQVR

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	1.95 RPM
bodymap2_adrenal	0.10 RPM	2.01 RPM
bodymap2_brain	0.00 RPM	2.18 RPM
bodymap2_breast	0.00 RPM	1.50 RPM
bodymap2_colon	0.00 RPM	3.60 RPM
bodymap2_heart	0.00 RPM	0.66 RPM
bodymap2_kidney	0.15 RPM	1.16 RPM
bodymap2_liver	0.06 RPM	0.65 RPM
bodymap2_lung	0.00 RPM	1.39 RPM
bodymap2_lymph_node	1.02 RPM	1.39 RPM
bodymap2_ovary	0.04 RPM	3.95 RPM
bodymap2_prostate	0.00 RPM	1.97 RPM
bodymap2_skeletal_muscle	0.02 RPM	2.62 RPM
bodymap2_testis	0.15 RPM	3.26 RPM
bodymap2_thyroid	0.15 RPM	4.11 RPM
bodymap2_white_blood_cells	0.18 RPM	2.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3843 was not detected

EST

No EST(s) were mapped for retro_hsap_3843 retrocopy.

TSS

No TSS is located nearby retro_hsap_3843 retrocopy 5' end.

Lab

retro_hsap_3843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3843 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2620
Gorilla gorilla	retro_ggor_2588
Macaca mulatta	retro_mmul_1616

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000243725	1 retrocopy	retro_hsap_3843 ,
Pongo abelii	ENSPPYG00000001312	1 retrocopy	retro_pabe_3055,
Pan troglodytes	ENSPTRG00000041368	1 retrocopy	retro_ptro_2620,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.25 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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