RetrogeneDB ID: retro_hsap_2224

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:242417739..242418405(+)
• Located in intron of: ENSG00000006607

Retrocopy information

• Ensembl ID: ENSG00000224232
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KCTD5
• Ensembl ID: ENSG00000167977
• Aliases: None
• Description: potassium channel tetramerization domain containing 5 [Source:HGNC Symbol;Acc:21423]

Sequence

>retro_hsap_2224
CTGCCACCTGCCTGGGGCAGCCTTAGGGCAGGGCTGGCGGGGGCGACCTGTGCTGCTGCAGTGCAAGACTCAGAGTGCCG
TGGCCCAGCACCCGGTAGCTTGTCCAAATGGCTCTGGCTCAACATTGGTGGCACCTACTTTCTCACCACCCAGCAGATGC
TGTGCCAGGACCTGAAATACTTCCTGTACTCCTTGTATCAGGCTAACCCCGACAAGGATGAAACTGTTGCCTATTTAATG
GACAGAGACCCCACCTATTTTGGGCCTGTGTTGAACTACCTGAGACGTGGCAAGCTGGTGATTAACAAAGACCTTGTGGA
GGAAGGAGTGTTGGAAAAAGCAGAATTTTACAGTATCACTTCATTAATAAAACTTGTAAAGGACAAAATTAGAGAACAAG
AGAGCAAAACATCACAGGTGCCCATGAAGCATGTGTACCACGTGCTTCAGTGTCAGGAGGAGGAACTCACACAGGTGGTG
TCCACCATGTCCGACAGCTGGAAGTTTGAACAACTGGTCAGCAATGGCTCTTCTTACAACTATGGGAATGAAGATCAGGC
CAAGTTCCTCTATGTGGTGTCCAAGAAACTTCACAACACCCCATACAGTATGGCCAGTGAACCCAGAAAGAAGGCCAAGA
TTTTGCAAGAACAAGGTTCAAGGATG

Alignment

ORF - retro_hsap_2224 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSPARGGIGAGLGGGLCRRCSAGLGALAQRPGSVSKWVRLNVGGTYFLTTRQTLCRDPKSFLYRLCQADP
          L.PA.G...AGL.G..C.............PGS.SKW..LN.GGTYFLTT.Q.LC.D.K.FLY.L.QA.P
Retrocopy LPPAWGSLRAGLAGATCAAAVQDSECRGPAPGSLSKWLWLNIGGTYFLTTQQMLCQDLKYFLYSLYQANP

Parental  DLDSDKDETGAYLIDRDPTYFGPVLNYLRHGKLVINKDLAEEGVLEEAEFYNITSLIKLVKDKIRERDSK
          ....DKDET.AYL.DRDPTYFGPVLNYLR.GKLVINKDL.EEGVLE.AEFY.ITSLIKLVKDKIRE..SK
Retrocopy ----DKDETVAYLMDRDPTYFGPVLNYLRRGKLVINKDLVEEGVLEKAEFYSITSLIKLVKDKIREQESK

Parental  TSQVPVKHVYRVLQCQEEELTQMVSTMSDGWKFEQLVSIGSSYNYGNEDQAEFLCVVSKELHNTPYGTAS
          TSQVP.KHVY.VLQCQEEELTQ.VSTMSD.WKFEQLVS.GSSYNYGNEDQA.FL.VVSK.LHNTPY..AS
Retrocopy TSQVPMKHVYHVLQCQEEELTQVVSTMSDSWKFEQLVSNGSSYNYGNEDQAKFLYVVSKKLHNTPYSMAS

Parental  EPSEKAKILQERGSRM
          EP..KAKILQE.GSRM
Retrocopy EPRKKAKILQEQGSRM

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	0.06 RPM	11.07 RPM
bodymap2_adrenal	0.12 RPM	16.01 RPM
bodymap2_brain	0.07 RPM	9.24 RPM
bodymap2_breast	0.00 RPM	5.97 RPM
bodymap2_colon	0.10 RPM	8.68 RPM
bodymap2_heart	0.02 RPM	5.87 RPM
bodymap2_kidney	0.00 RPM	11.21 RPM
bodymap2_liver	0.00 RPM	10.94 RPM
bodymap2_lung	0.00 RPM	9.39 RPM
bodymap2_lymph_node	0.00 RPM	18.29 RPM
bodymap2_ovary	0.17 RPM	13.20 RPM
bodymap2_prostate	0.19 RPM	13.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	9.80 RPM
bodymap2_testis	0.41 RPM	14.57 RPM
bodymap2_thyroid	0.08 RPM	10.19 RPM
bodymap2_white_blood_cells	0.00 RPM	34.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2224 was not detected

EST

No EST(s) were mapped for retro_hsap_2224 retrocopy.

TSS

No TSS is located nearby retro_hsap_2224 retrocopy 5' end.

Lab

retro_hsap_2224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2224 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1685
Gorilla gorilla	retro_ggor_1752
Pongo abelii	retro_pabe_2093

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019357	1 retrocopy	retro_cfam_433,
Homo sapiens	ENSG00000104756	4 retrocopies	retro_hsap_1730, retro_hsap_3305, retro_hsap_4037, retro_hsap_4156,
Homo sapiens	ENSG00000167977	1 retrocopy	retro_hsap_2224 ,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Monodelphis domestica	ENSMODG00000016596	1 retrocopy	retro_mdom_506,
Sarcophilus harrisii	ENSSHAG00000006867	1 retrocopy	retro_shar_158,
Ictidomys tridecemlineatus	ENSSTOG00000006647	8 retrocopies	retro_itri_1562, retro_itri_1690, retro_itri_1692, retro_itri_1761, retro_itri_1779, retro_itri_1844, retro_itri_1889, retro_itri_950,
Tursiops truncatus	ENSTTRG00000008237	1 retrocopy	retro_ttru_1510,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 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	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 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	0.03 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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