RetrogeneDB ID: retro_pabe_3823

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:151626381..151627233(-)
• 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_3823
ATGAGCTCCACACAATTCAACAAGGGGCCCTTGTACAGCTCTTGGTCAAGGTCAAGAACCAGCTCCTGCTGAAATACATC
GCTCAGAAGGAGGCTGATCTCCCCAGGTGGATTGAGGGACTCATGGGCTTCTCTATTGGCCCCAACTTCCAGAAGGATCT
GAAGGACGGGATTATTTCATGCACACTCATGAACAAGCTCCAACAGGCTCAGTCTCCAAAGTCAACCACTCTATGCAGAG
CTAGCACCAGCTAGAAAACCTCTCCAACTTCATCAAGTCCGTGGTTAGCTATGGCATGAACCCTGTGGACCTGTTTAAGG
CCAATGACCTGTTTGAGAGTGTGAACATGACACATCTGCAGGTGTCTCTTCTAGCCCTGGCGGGGAAGACCAAGACAAAG
GGGCTTCAGAATGTTGTGGACATTAGCACCAAATACTCAGAGAAGCAGGAGCAGAACTTGTACAATGCCACCATGAAGGC
TGACCAGTATATCACTGGGCTGCAGACAGGCACAAACAAATGTGCCAGCCAGCCCAGCATGACAGCTTATAGCATGAAGG
GGCATCTCTTTGACCCCAAGAACTATATCTGTCCCCCATGGATCTACTGACCATCAGTCTCCAGATGGGTACAAACAAAT
GTGCCAGCCAGGTGGGCATAACAGTTCTTGGGACCTGGAGGCACATCTGTGACAACAAGCTGGGAACTGACAAGTGGGAC
AACTCCATGTCCCTGCAGATGGGCTACACACAGGGTGCCAACCAGAGCAGCCAGGTCTTTGGCCTGGGTCAACAGATATA
TGATCCCAAGTACTGCCTGTAAGGCCCAGTGGCTACTTCCCAGGCCCAAGGG

Alignment

ORF - retro_pabe_3823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.7 %
• Parental protein coverage: 92.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYG-LSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQP
          MSSTQFNKGP.Y..L...VKN.LL.KY..QKEA.L..WIEGL.G.SIGP.FQK.LKDG.I.CTLMNKLQ.
Retrocopy MSSTQFNKGPLYS<LLVKVKNQLLLKYIAQKEADLPRWIEGLMGFSIGPNFQKDLKDGIISCTLMNKLQQ

Parental  -GSVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQS
          .GSV.K.N.SMQ..HQLENLSNFIK..VSYGMNPVDLF.ANDLFES.NMT..QVSLLALAGK.KTKGLQ.
Retrocopy <GSVSKVNHSMQS*HQLENLSNFIKSVVSYGMNPVDLFKANDLFESVNMTHLQVSLLALAGKTKTKGLQN

Parental  GVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILP-PMDHSTIS
          .VDI..KYSEKQE.N...ATMKA.Q...GLQ.GTNKCASQ..MTAY....HL.DPKN.I.P.PMD..TIS
Retrocopy VVDISTKYSEKQEQNLYNATMKADQYITGLQTGTNKCASQPSMTAYSMKGHLFDPKNYICP<PMDLLTIS

Parental  LQMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQG
          LQMGTNKCASQVG.T..GT.RHI.D.KLGTDK.DN.SMSLQMGYTQGANQS.QVFGLG.QIYDPKYC..G
Retrocopy LQMGTNKCASQVGITVLGTWRHICDNKLGTDKWDN-SMSLQMGYTQGANQSSQVFGLGQQIYDPKYCL*G

Parental  TVADGAPSG
          .VA.....G
Retrocopy PVATSQAQG

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_3823 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3823 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,