RetrogeneDB ID: retro_ptro_2648

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:118460558..118461293(-)
• Located in intron of: ENSPTRG00000019616

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSPTRG00000010637
• Aliases: None
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_ptro_2648
ATGGCTGGGATCACCACCATCGAGGCGGTTAAGGGCAATATCCAGGTTATGCAGCAGCAGGCAGATGATGCAGAGGAGCG
AGCTGATCGTCTCCAGTGAGAAGTTGAGGGAGAAAGGTGTTCCCAGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACC
GTAGGATCCAGCTGGTTCATGAGAAGCTGGACTGTGCTCAGGAGTGCCCAGCCACTGCCCTGCAAAAGCTGGAAGAAGCA
GAAAAAACTGATGAGAGTGAGAGAGGTATGAAGTTTATTGAAAACCAGCCCTTAAAAGATGAAGAAAAGATGGAGCTCCA
GGAAATTCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAAATAGGAAGTATGAAGAGGTAGCTCATAAGTTGGTGA
TCATTGAAAGAGACTTGGAACGCACAGAGGAACAAACTGAGCTGGCAGAGTACCGTTGCCGAGAGATGGATGAGCAGATC
AGACTGATGGACCAGAATCTGAAGTGTCTGAGTCCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATGAGAAAGA
GATCAAGATTCTTACTGATAAATTCAAGGAGGGAGAGACCCGTGATGGGTTTGCTGAGAGACTGGTAGCCAAGCTGGAAA
ATACAATTGAAGACCTGGAAGATAAACTCAAATGCACCAAAGGACAGCGCCTCTGTACACAAAAGATGCTGGTCCAGACT
CTGCTTGACCTGAAT

Alignment

ORF - retro_ptro_2648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.13 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLNSLEAVKRKIQALQQQADEAEDRAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERL
          MAG....EAVK..IQ..QQQAD.AE.RA..LQ.E..GER...E.AE..VA.LNRRIQLV.E.LD.AQE..
Retrocopy MAGITTIEAVKGNIQVMQQQADDAEERADRLQ*EVEGERCSQEQAEAEVASLNRRIQLVHEKLDCAQECP

Parental  ATALQKLEEAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGEL
          ATALQKLEEAEK..DESERGMK.IEN...KDEEKME.QE.QLKEAKHIAEEA.RKYEEVA.KLVI.E..L
Retrocopy ATALQKLEEAEKT-DESERGMKFIENQPLKDEEKMELQEIQLKEAKHIAEEANRKYEEVAHKLVIIERDL

Parental  ERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTV
          ER.EE..E..E..C....E.......NLK.L..A.EKYS.KEDKYE.EIK.L.DK.KE.ETR..FA....
Retrocopy ERTEEQTELAEYRCREMDEQIRLMDQNLKCLSPAEEKYSQKEDKYEKEIKILTDKFKEGETRDGFAXXXX

Parental  AKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELN
          .................K.........L.QTL..LN
Retrocopy XXXXXXXXXXXXXXXXTKGQRLCTQKMLVQTLLDLN

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	0.05 RPM	31.82 RPM
SRP007412_cerebellum	0.22 RPM	94.89 RPM
SRP007412_heart	0.35 RPM	42.12 RPM
SRP007412_kidney	0.24 RPM	39.70 RPM
SRP007412_liver	0.00 RPM	22.91 RPM
SRP007412_testis	0.00 RPM	32.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2648 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2648 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3893
Gorilla gorilla	retro_ggor_2621

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Pan troglodytes	ENSPTRG00000010637	10 retrocopies	retro_ptro_1002, retro_ptro_1109, retro_ptro_1341, retro_ptro_1342, retro_ptro_1750, retro_ptro_1768, retro_ptro_2648 , retro_ptro_2694, retro_ptro_2830, retro_ptro_516,
Pteropus vampyrus	ENSPVAG00000009755	2 retrocopies	retro_pvam_186, retro_pvam_187,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tarsius syrichta	ENSTSYG00000010642	9 retrocopies	retro_tsyr_1377, retro_tsyr_1613, retro_tsyr_1642, retro_tsyr_1853, retro_tsyr_628, retro_tsyr_694, retro_tsyr_704, retro_tsyr_742, retro_tsyr_749,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,