RetrogeneDB ID: retro_hsap_1168

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:19300841..19301582(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000204718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSG00000064666
• Aliases: None
• Description: calponin 2 [Source:HGNC Symbol;Acc:2156]

Sequence

>retro_hsap_1168
GTAAGCTCCACGCAGTTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGACGTCCAGAACCGGCTCCTGTCCATATATGA
CTCGCAGAAGGAGGTAGAGCTCCGCAGCTGGATCTAGGGACTCACCGGCCTCTCCATCGGCCCAGTGAGTCCCGACTTCC
AGAAGGGCCTGAAGGACGGGATTATCTTATGCACACTCATGAACAAACTGCAGCCGGGCTCAGTCCCCAAAATCAACCGC
TTCAGCAGAACTGGTACCAGCTAGAAACCCTCTCCAACCTCCTCAAGTCCATGGTCAGCTACAGCATGAACCCCGTGGAC
CTATTTGAGACTAACGACCTGTTTTAGAGTGGGAACGTGAGGCAGGTGCAGGTGTCTCTTCTCGCCCTGGCAGGGAAGGC
CAAGACTAAGGGGCTGCAGAGCGAGGTGGACATCCGTGAGGAGTACTCAGAGAAGCAGGAGGGGAACTTCGACGACGCCA
CCATGAAGGCTGGCCAGTGCGTCATCGGGCTGCAGATTACCAACAAACGCGCCAGCCAGTCAGGCACGACTGTGTACGGC
AGAGCACGAGGAGGCATCTCTACGATCCCAAGAACAACATCCTGCCCCCCATGGACCACTCGACCATCAGCCTCCAGATG
GGTACAAGCAAGTGCGCCAGCCAGGTGGGCATGGCGGCTCCCAGGACCCGGTGGCACATCTACGACACGAAGCTGGGAAT
CACAAGTATGACAACTCTTCA

Alignment

ORF - retro_hsap_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 78.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIG---PDFQKGLKDGTILCTLMNKL
          .SSTQFNKGPSY.L.A.V.NRLLS.YD.QKE.ELR.WI.GLTGLSIG...PDFQKGLKDG.ILCTLMNKL
Retrocopy VSSTQFNKGPSYRLLADVQNRLLSIYDSQKEVELRSWI*GLTGLSIGPVSPDFQKGLKDGIILCTLMNKL

Parental  QPGSVPKINRS-MQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGL
          QPGSVPKINR...QNW.QLE.LSN..K.MVSY.MNPVDLFE.NDLF.SGN..QVQVSLLALAGKAKTKGL
Retrocopy QPGSVPKINRF<QQNWYQLETLSNLLKSMVSYSMNPVDLFETNDLF*SGNVRQVQVSLLALAGKAKTKGL

Parental  QSGVDIGVKYSEKQERNFDDATMKAGQCVIGLQ-MGTNKCASQSGMTA-YGTRRHLYDPKNHILPPMDHS
          QS.VDI...YSEKQE.NFDDATMKAGQCVIGLQ...TN..ASQ........TRRHLYDPKN.ILPPMDHS
Retrocopy QSEVDIREEYSEKQEGNFDDATMKAGQCVIGLQ>LPTNAPASQARLCT>QSTRRHLYDPKNNILPPMDHS

Parental  TISLQMGTNKCASQVGMTAPGTRRHIYDTKL-GTDKCDNSS
          TISLQMGT.KCASQVGM.AP.TR.HIYDTKL.G..K.DNSS
Retrocopy TISLQMGTSKCASQVGMAAPRTRWHIYDTKL<GNHKYDNSS

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	112.57 RPM
bodymap2_adrenal	0.00 RPM	74.98 RPM
bodymap2_brain	0.00 RPM	7.85 RPM
bodymap2_breast	0.00 RPM	71.30 RPM
bodymap2_colon	0.02 RPM	53.46 RPM
bodymap2_heart	0.00 RPM	21.03 RPM
bodymap2_kidney	0.00 RPM	45.66 RPM
bodymap2_liver	0.00 RPM	12.93 RPM
bodymap2_lung	0.00 RPM	217.30 RPM
bodymap2_lymph_node	0.00 RPM	138.72 RPM
bodymap2_ovary	0.00 RPM	182.32 RPM
bodymap2_prostate	0.00 RPM	86.83 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.91 RPM
bodymap2_testis	0.02 RPM	39.76 RPM
bodymap2_thyroid	0.00 RPM	73.44 RPM
bodymap2_white_blood_cells	0.00 RPM	341.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1168 was not detected

EST

No EST(s) were mapped for retro_hsap_1168 retrocopy.

TSS

No TSS is located nearby retro_hsap_1168 retrocopy 5' end.

Lab

retro_hsap_1168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1168 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1247

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000064666	16 retrocopies	retro_hsap_1168 , retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 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	0.03 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 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	0.02 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	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.07 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).