RetrogeneDB ID: retro_pabe_1920

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:3043454..3044380(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1920
GTAAGCTCCACTCAGTTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGAAGTCCAGAACCGGCTTCTGTCCAGATATGA
CTCCCAGAAGGAGGTAGAGCTCCGCAGCTGGATCTAGGGACTCACCGGCGTCTCCATCGGCCCGACTTCCAGAAGGGCCT
GAAGGACGGGATTATTTTATGCACACTCATGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACTGCTTCAGTGTAG
AACTGCTACCAGCTAGAAAACCTCTCCAACTTCCTCAAGGCCATGGTCAGCTACAGCATGAACCCCGTGGACCTATTTGA
GGCCACGACCTGTTTGAGAGTGGGAACGTGAGGCAGGTGCAGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCAAGACTAA
GGGGCTGCAGAGAGAGGTGGACATCGGTGAGGAGTACTCAGAGAAGCAGGAGCGGAACTTCGACGACGCCACCATGAAGG
CTGGCCAATGCGTCATCGGGCTGCAGATTACCAACAAATGCGCCAGCCAGTCAGGCATGACTGTGTACGGCAGAGCATGA
GGAGGCATCTCTACGACCCCAAGAACCACTTGCTGCCCCCCGCGGACCACTCGACCATCACCCTCCAGATGGGTACAAGC
AAGTGCGCCAGCCAGGTGAGCATGGCAGCTCCCGGGACCCAGAGGCACATCTACGACACGAAGCTGGGAATCACAAGTAT
GACAACTCTTCCATGTCCCTGAAGATGGGCTACACGCTGGGCACCAACCAGAGCGGCCAGGTCTTCAGCCTGGGCCGACA
GATACACGACCCCAAGTACTGCCTGGGAGAGCAGTGGCCCACGGGGCTCCCTCGGGTGCAGGTGACTGACCGGGGCCAGG
GGAGGCCCCTCAATATCTCCCTTACTACCAAGAGGAGACCGGGTAC

Alignment

ORF - retro_pabe_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGP-DFQKGLKDGTILCTLMNKLQP
          .SSTQFNKGPSY.L.AEV.NRLLS.YD.QKE.ELR.WI.GLTG.SIGP.DFQKGLKDG.ILCTLMNKLQP
Retrocopy VSSTQFNKGPSYRLLAEVQNRLLSRYDSQKEVELRSWI*GLTGVSIGP<DFQKGLKDGIILCTLMNKLQP

Parental  GSVPKIN-RSMQNWHQLENLSNFIKAMVSYGMNPVDLFEA-NDLFESGNMTQVQVSLLALAGKAKTKGLQ
          GSVPKIN..S..N..QLENLSNF.KAMVSY.MNPVDLFEA..DLFESGN..QVQVSLLALAGKAKTKGLQ
Retrocopy GSVPKIN>ASV*NCYQLENLSNFLKAMVSYSMNPVDLFEA<HDLFESGNVRQVQVSLLALAGKAKTKGLQ

Parental  SGVDIGVKYSEKQERNFDDATMKAGQCVIGLQ-MGTNKCASQSGMTA-YGTRRHLYDPKNHILPPMDHST
          ..VDIG..YSEKQERNFDDATMKAGQCVIGLQ...TN..ASQ.........RRHLYDPKNH.LPP.DHST
Retrocopy REVDIGEEYSEKQERNFDDATMKAGQCVIGLQ>LPTNAPASQA*LCT>QSMRRHLYDPKNHLLPPADHST

Parental  ISLQMGTNKCASQVGMTAPGTRRHIYDTKL-GTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYC
          I.LQMGT.KCASQV.M.APGT.RHIYDTKL.G..K.DNSSMSL.MGYT.G.NQSGQVF.LGRQI.DPKYC
Retrocopy ITLQMGTSKCASQVSMAAPGTQRHIYDTKL<GNHKYDNSSMSLKMGYTLGTNQSGQVFSLGRQIHDPKYC

Parental  -PQGTVADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
          .P...VA.GAPSG.GD.P.PGE.P.Y.PYYQEE.GY
Retrocopy <PGRAVAHGAPSGAGD*PGPGEAPQYLPYYQEETGY

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	0.00 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_1920 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1920 has 0 orthologous retrocopies within eutheria group .

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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,