RetrogeneDB ID: retro_mmus_1625

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:21967497..21968242(-)
• Located in intron of: ENSMUSG00000053347

Retrocopy information

• Ensembl ID: ENSMUSG00000086869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tpm4
• Ensembl ID: ENSMUSG00000031799
• Aliases: Tpm4, 2610528G24Rik
• Description: tropomyosin 4 [Source:MGI Symbol;Acc:MGI:2449202]

Sequence

>retro_mmus_1625
ATGGCCGGCCTCAACTCACTGGAGGCAGTGAAGCACAAGATCCAGGCCCTGCAGCAGCAGGCAGACGATGCAGAGAATAG
TGCGCAGGGCCTGCATTGCGGAACTGGAAGGCGAGCACGAGCGGCGGGAGAAATCTGAAGGAGATGCAGCCGCTCTCAAC
CGCTGCATCCAACTGCTGGAGGAGGAACTGGACCTGGCTCAGGAGCAGCTGGCCATAGCCCTGCAGAATCTGGAAGAGGC
AGAGAAGGCTGCTGATGAGAGTGAGAGAGGCGTGAAGGTAATAGAGAACCGAGCCATGAAAGATGAGGAAAAGATGGAGA
TCCTGGAGATGCAGCTCAAAGAAGCCAAGCACATCACTGAGGAGGCCGACCGCAAGTACGAGGAGGTCGCTCATAAGTTG
GTCATCCTGGAGGGTGAGCTGAAGAGAGCAGAGGAGCGGGCGGAGGTATCTGAACTAAAGTGTGGTGACCTGGAAGAAGA
GCTCAAGTATGTAACTAACAATCTGAAATCACTGGAGGCTGCTTCTGAAAAGTATTCTGAAAAGGAGGATAAATATGAAG
AAGAAATCAAGCTTCTGTCTGACAAGCTGAAGGAGGCTGAGACCCGAGCTGAGTTTGCAGAAAGGACAGTTTCTAAACTG
GAGAAGACAATCGATGACCTGGAAGAAAAACTTGCCCAGGCCAAAGAAGAGAATGTGGGCTTACATCAGACACTGGACCA
GACACTAAACGAACTTAACTGTATA

Alignment

ORF - retro_mmus_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLNSLEAVKRKIQALQQQADDAEDRAQGLQ-RELDGERERREKAEGDAAALNRRIQLLEEELDRAQEQ
          MAGLNSLEAVK.KIQALQQQADDAE..AQGL...EL.GE.ERREK.EGDAAALNR.IQLLEEELD.AQEQ
Retrocopy MAGLNSLEAVKHKIQALQQQADDAENSAQGLH>AELEGEHERREKSEGDAAALNRCIQLLEEELDLAQEQ

Parental  LATALQNLEEAEKAADESERGMKVIENRAMKDEEKMEILEMQLKEAKHITDEADRKYEEVARKLVILEGE
          LA.ALQNLEEAEKAADESERG.KVIENRAMKDEEKMEILEMQLKEAKHIT.EADRKYEEVA.KLVILEGE
Retrocopy LAIALQNLEEAEKAADESERGVKVIENRAMKDEEKMEILEMQLKEAKHITEEADRKYEEVAHKLVILEGE

Parental  LKRAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERT
          LKRAEERAEVSELKCGDLEEELK.VTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERT
Retrocopy LKRAEERAEVSELKCGDLEEELKYVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERT

Parental  VSKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI
          VSKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI
Retrocopy VSKLEKTIDDLEEKLAQAKEENVGLHQTLDQTLNELNCI

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	0.12 RPM	20.35 RPM
SRP007412_cerebellum	0.61 RPM	23.71 RPM
SRP007412_heart	0.47 RPM	74.12 RPM
SRP007412_kidney	1.52 RPM	65.66 RPM
SRP007412_liver	0.19 RPM	17.31 RPM
SRP007412_testis	0.37 RPM	6.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1625 was not detected

EST

No EST(s) were mapped for retro_mmus_1625 retrocopy.

TSS

No TSS is located nearby retro_mmus_1625 retrocopy 5' end.

Lab

retro_mmus_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 44 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	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
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,