RetrogeneDB ID: retro_ptro_1341

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:58339679..58340417(+)
• Located in intron of: None

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_1341
ATGGCTGGGATCACCACCATCGAGGCAGTGAAGCGCAAGATCCAGGTTCTGCAGCACCAGGCAGATGATGCAGAGGAGTG
AGCTGAGCACCTCCAGTGAGAAGCTGAGGGAAAAAGGTGGGCCTGGGAACAGGCTGAGGCTGAGGTGGCCTCCGTGAACG
GTAGGATCCAGCTGGTTGAAGAGGAGCTGGACTGTGCTCAGGAGCGCCTGACCACTGCCCTGCAAAAGCTGGAAGAAGCG
GGAAAAGCAGCTGATGAGAGTGAGAGAGATATAAAGGTTACTGAAAACCGGGCCTTAAAAGATGAAGAAAAGATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGATGAGGCAGATGGGAAGTATGAAGAGGTGGCTCGTAAGTTGG
TGATCATTGAAAGAGACATGGAATGCACAGAAGAACGAGCTGAGCTGGCAGAGTCCCATTGTTGAGAGATGGATGAGCAG
ATCAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCAGCTGAAGAAAACTACCCTCAAAAAGAAGACAAACGTGAGGA
AGAGATGAAGATTCTTTCTGATAATCTCAAGGAGGCAGAGACCCATGCTGAGTTGGCTGAGAGATCAGTAGCCAAGCTGG
AAAAGACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAAGAAGAACACCTCTGTACACAAAGGATGCTGGACCAG
ACTCTGCTTGACCTGAAT

Alignment

ORF - retro_ptro_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLNSLEAVKRKIQALQQQADEAEDRAQGLQRELDGERERREKAEGDVAALNRRIQLVEEELDRAQERL
          MAG....EAVKRKIQ.LQ.QAD.AE..A..LQ.E..G.R...E.AE..VA..N.RIQLVEEELD.AQERL
Retrocopy MAGITTIEAVKRKIQVLQHQADDAEE*AEHLQ*EAEGKRWAWEQAEAEVASVNGRIQLVEEELDCAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGEL
          .TALQKLEEA.KAADESER..KV.ENRA.KDEEKME.QE.QLKEAKHIA.EAD.KYEEVARKLVI.E...
Retrocopy TTALQKLEEAGKAADESERDIKVTENRALKDEEKMELQEIQLKEAKHIADEADGKYEEVARKLVIIERDM

Parental  ERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTV
          E..EERAE..E..C....E.......NLK.L.AA.E.Y..KEDK.EEE.K.LSD.LKEAET.AE.AER.V
Retrocopy ECTEERAELAESHC*EMDEQIRLMDQNLKCLSAAEENYPQKEDKREEEMKILSDNLKEAETHAELAERSV

Parental  AKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELN
          AKLEKTIDDLE.KL...KEE.......LDQTL..LN
Retrocopy AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLN

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	0.16 RPM	31.82 RPM
SRP007412_cerebellum	0.39 RPM	94.89 RPM
SRP007412_heart	0.09 RPM	42.12 RPM
SRP007412_kidney	0.24 RPM	39.70 RPM
SRP007412_liver	0.29 RPM	22.91 RPM
SRP007412_testis	0.95 RPM	32.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1341 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1341 has 0 orthologous retrocopies within eutheria group .

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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,