RetrogeneDB ID: retro_pabe_1299

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:54849645..54850573(-)
• Located in intron of: ENSPPYG00000006508

Retrocopy information

• Ensembl ID: ENSPPYG00000006509
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSPPYG00000009302
• Aliases: CNN2, Calponin-2
• Description: Calponin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFN6]

Sequence

>retro_pabe_1299
ATGAGTTCCACGCAGTTCAACAAGGGCCTCTAGTATGGGCTGTCAGCCGAGGTCAAGAACTGGCTTCTGCCCAAATATGA
CCCCCAGAAGGAGGCAGAGCTCCGCAGCTGGATCAAGGGACTCACCGGCATCTCCATTGATCCTGACTTCCAGAAGAGCC
TGAAGGATGGGATTATCTTATGCATACTCATTAACAAGCTGCAGCTGGCCTCAGTCCCCAAGATCAACCATTCCATGCAG
AAGTGGCAGCAGCTAGAAAACCTCTCCCACTTCATCAAGGCCATGGTCAGCTATGACATGAACCCCATGGACGTGTTCGA
GGCCAACAACCTGTTTGAGAGTGGGAACATGAGGCACATGCAGGTGTCTCTTTTTGCCCTAGCAGGGAAGGCCAAGACTA
AGGGGCTGCAGAGCGGGGTGGACACTGGCATCAAGTACTCAGAGAAGCAGGAGCAGAACTTCAGGGACGCCGCCATGAAG
GCTGGCCAGTGCGTCATCGGGCTGCAGATGGGCACCAACAAATGTGCCAGCCAGTTGGGCATGACTGTGTATGGCGTGAG
GAGGCATCTGTGTGACCCCAAGAATCACATCCTGTCCCCCATGGACCACTCGGCCATTAGCCTCCAGATGGGTACAAATA
AGTGTGCCAGCCAGGTGAGCATCACGGCTCCTGGGACGTGGCGGCACATCGATGACACCAAGCTGGGAACCGACAAGTGT
GATAATTCCTCCATGTCCCTGCAGATGGGCTACACCCAGGGTACCAACCATAGTAGCCAGGGTCTTTGGCCTGGGCCAGC
ATATATATGACCCCAAGTACTGCCCGCCAGGCACAATGGCCGACGGGGCTTCCCTGGGCGCTGGCGACTGCCTGGGCCCA
GGAGAGGTCCCTGAATATCCCCCTTACTACCAGGAGGAGGCTGGCTAC

Alignment

ORF - retro_pabe_1299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPG
          MSSTQFNKG..YGLSAEVKN.LL.KYDPQKEAELR.WI.GLTG.SI.PDFQK.LKDG.ILC.L.NKLQ..
Retrocopy MSSTQFNKGL*YGLSAEVKNWLLPKYDPQKEAELRSWIKGLTGISIDPDFQKSLKDGIILCILINKLQLA

Parental  SVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSGV
          SVPKIN.SMQ.W.QLENLS.FIKAMVSY.MNP.D.FEAN.LFESGNM...QVSL.ALAGKAKTKGLQSGV
Retrocopy SVPKINHSMQKWQQLENLSHFIKAMVSYDMNPMDVFEANNLFESGNMRHMQVSLFALAGKAKTKGLQSGV

Parental  DIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISLQM
          D.G.KYSEKQE.NF.DA.MKAGQCVIGLQMGTNKCASQ.GMT.YG.RRHL.DPKNHIL.PMDHS.ISLQM
Retrocopy DTGIKYSEKQEQNFRDAAMKAGQCVIGLQMGTNKCASQLGMTVYGVRRHLCDPKNHILSPMDHSAISLQM

Parental  GTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQ-VFGLGRQIYDPKYCPQGTV
          GTNKCASQV..TAPGT.RHI.DTKLGTDKCDNSSMSLQMGYTQG.N.S.Q.VFGLG..IYDPKYCP.GT.
Retrocopy GTNKCASQVSITAPGTWRHIDDTKLGTDKCDNSSMSLQMGYTQGTNHSSQ>VFGLGQHIYDPKYCPPGTM

Parental  ADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
          ADGA..G.GDC..PGEVPEYPPYYQEEAGY
Retrocopy ADGASLGAGDCLGPGEVPEYPPYYQEEAGY

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.62 RPM
SRP007412_cerebellum	0.00 RPM	3.53 RPM
SRP007412_heart	0.03 RPM	19.99 RPM
SRP007412_kidney	0.00 RPM	88.20 RPM
SRP007412_liver	0.00 RPM	41.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1299 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1299 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1575
Pan troglodytes	retro_ptro_1061
Gorilla gorilla	retro_ggor_1199

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612,
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581,
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,
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,
Myotis lucifugus	ENSMLUG00000013160	4 retrocopies	retro_mluc_1536, retro_mluc_1965, retro_mluc_2047, retro_mluc_2210,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
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,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326,