RetrogeneDB ID: retro_ptro_1554

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:94872073..94872894(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSPTRG00000000979
• Aliases: CNN3, calponin-3
• Description: None

Sequence

>retro_ptro_1554
TTCAACAAGGGACCCGCCTACAGGCTCTTGGCGGACGTCCAGAACAGGCTTCTGTCCAAATATGACTCCCAGAAGGAGGC
AGAGCTCCGCAGCTGGATCAAGGGATTCACTGGCCTCTCCATCTGCCCCAACTTCCAGAAGGGCCTGAAGGACGAGATTA
TTTTATGCACACTCGTGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACGGTTTCCGTGTAGAACTGGCACCAGCT
AGAAAACCTCTCCAACTTCCTCAAGGCAATGGTCAGCTACGGCATGATCCCGTGGACCTATTTGAGGCCAACGACCTGTT
TGAGAGTGGGAACAATATGCAGGTGCGGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCACAAGACTAAGGGGCTGCAGAG
CGGGGTGGACATCCGTGACAAGTACTCAGAGAAGCAGAACTTCGACGACACCACCATGAAGGCCAGCCTGTGCGTCATCC
GGCTGCAGATTACCAACAAATGTGCCAGCCAGTCAGGCATGACCGCATACGGCACGAGGAGGCATCTCTACGACCCCAAG
AACCGCATCCTGCCCCCCATGGACAACTTGATCATCAGCCTCCGGATGGGTACAAACAAGTGCGCCAGCCAGGTGGGCAT
GACGGCTCCCGGGAACCAGCGGCACATCTATGACACCAAGTTGCGAATCGACAAGTGTGAGAACTCCTCCATGTCCCTGA
AGATGGGCTACACGCAGGTCGCCAATCACAGCGGACAGGTCTTTGGCCTAGGCCGGCAAATATATGAACCCAAGTACTAG
CCGGGTGGCCCAGTGGCCCAC

Alignment

ORF - retro_ptro_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.3 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKV
          FNKGP.Y.L.A.V.N...SKYD.Q.E..LR.WI...TG.SI..NFQ.GLKD.IILC.L.NKLQPGSV.K.
Retrocopy FNKGPAYRLLADVQNRLLSKYDSQKEAELRSWIKGFTGLSICPNFQKGLKDEIILCTLVNKLQPGSVPKI

Parental  N-ESSLNWPQLENIGNFIKAIQAYGM-KPHDIFEANDLFENGNMTQVQTTLVALAGLA-KTKG-FHTTID
          N..S..NW.QLEN..NF.KA...YGM..P.D.FEANDLFE.GN..QV...L.ALAG.A....G......D
Retrocopy N>VSV*NWHQLENLSNFLKAMVSYGM<DPVDLFEANDLFESGNNMQVRVSLLALAGKATRLRG<LQSGVD

Parental  IGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMG
          I..KY.EKQ...FD....KA...VI.LQ..TNKCASQ.GMTAYGTRRHLYDPK.....P.D...ISL.MG
Retrocopy IRDKYSEKQ--NFDDTTMKASLCVIRLQI-TNKCASQSGMTAYGTRRHLYDPKNRILPPMDNLIISLRMG

Parental  TNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEP
          TNK.ASQ.GM.APG..R.IYD.KL......NS..SL.MG...VA...G..V.GLGRQ.Y.PKY...P..P
Retrocopy TNKCASQVGMTAPGNQRHIYDTKLRIDKCENSSMSLKMGYTQVANHSG-QVFGLGRQIYEPKY--*PGGP

Parental  VIH
          V.H
Retrocopy VAH

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	37.13 RPM
SRP007412_cerebellum	0.00 RPM	64.38 RPM
SRP007412_heart	0.00 RPM	25.77 RPM
SRP007412_kidney	0.00 RPM	191.01 RPM
SRP007412_liver	0.00 RPM	31.03 RPM
SRP007412_testis	0.00 RPM	79.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1554 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1554 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4269

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554 , retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,