RetrogeneDB ID: retro_hsap_255

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:166765502..166766110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232223
• 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_255
ATGAGTTCCACGCAGTTCAACAAGGGGCCTTCTTACCAGCTTTTTGCCGAGATCAAGAACCAGCTCCTGTTCAAATGCGA
CCCTCAGAAGCAGGCGGCGCTCTGCAGCTGGATCGAGGGACTCACCCGCCTCTCTTTCAGCCCCGACTTCCAGAAGAGTC
TGAAGGAAGGGATTGTCTTATGCACACTCATGAACAAGCTGGGCTCAGTCCCCAAGATCAACGGCTCATGCAGAACTGGC
ACCAGCTAGAAAATCTCTCCAACTTCATCAAGGCCATGGTTGGATACGACATGAACCCCATGGACCTGTTCGAGGCCAAC
GACCTGTTTGAGAGTAGGAACATGACGCAGGTGCAGCTGTCTCTTCTAGCCCTGGCAGGGAAGGTCAAGACAAAGCTGCT
GCAGAATGGGGTGGACGTCGGGGTCAAATACTCGGAGAAGCAGGAGCGGAACTTCGACGACGCCACCTTGAAGGCCAGCC
AGTGCCTCACTGAGCTGCAGATGGGCACCAACATATGTGCCTGCCAGTCGGGCGCGACAACTTAGGGCACGATGAGGCAT
CTCTACCACCCCAAGAACCGTATCCTGCCCTCTGGACCACTCGACCAT

Alignment

ORF - retro_hsap_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 65.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPG
          MSSTQFNKGPSY.L.AE.KN.LL.K.DPQK.A.L..WIEGLT.LS..PDFQK.LK.G..LCTLMNKL..G
Retrocopy MSSTQFNKGPSYQLFAEIKNQLLFKCDPQKQAALCSWIEGLTRLSFSPDFQKSLKEGIVLCTLMNKL--G

Parental  SVPKIN-RSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSG
          SVPKIN.R.MQNWHQLENLSNFIKAMV.Y.MNP.DLFEANDLFES.NMTQVQ.SLLALAGK.KTK.LQ.G
Retrocopy SVPKIN<RLMQNWHQLENLSNFIKAMVGYDMNPMDLFEANDLFESRNMTQVQLSLLALAGKVKTKLLQNG

Parental  VDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILP--PMDH
          VD.GVKYSEKQERNFDDAT.KA.QC...LQMGTN.CA.QSG.T..GT.RHLY.PKN.ILP..P.DH
Retrocopy VDVGVKYSEKQERNFDDATLKASQCLTELQMGTNICACQSGATT*GTMRHLYHPKNRILPSGPLDH

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	0.00 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	0.00 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 activity near the 5' end of retro_hsap_255 was not detected

EST

No EST(s) were mapped for retro_hsap_255 retrocopy.

TSS

No TSS is located nearby retro_hsap_255 retrocopy 5' end.

Lab

retro_hsap_255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_255 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_305
Pongo abelii	retro_pabe_407

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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,