RetrogeneDB ID: retro_btau_1604

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:31871416..31872129(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000012916
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSBTAG00000004553
• Aliases: None
• Description: tropomyosin alpha-4 chain [Source:RefSeq peptide;Acc:NP_001094632]

Sequence

>retro_btau_1604
GTGAAACGCAAGATCCAGGCCCTGCAGCAGCAAGCAGATGAGGCGGAGGACCGCGCGCAGGGCCTGCAGCGCGAGCTGGA
CGGCAGGGCGAGCGGCGCGAGAAAGCCGAAGGTGATGTGGCAGCTCTCAATCGGTGCATCCAGCTCGTTGAGGAGGAGTT
GGACAGGGCCCAGGAACGACCGGCCACAGCCCTGCAGAAGCTGAAGGAGGCAGAAAAGGCTGCAGATGAGAGTGAGAGAG
GGATGAAGGTGATAGGAAACCGCGCCATGAAAGATGAGGAGAAGATGGAGATTCAGGAGATGCAGCTTAAAGAGGCCAAA
CACATTGCCGAGGAGGCTGACCGCAAATACGAAGAGGTAGCTCGAAAGTTGGTCATCCTGGAGGGTGAGCTAGAGAGGGC
AGAGGAGTGTGCCGAGGTGTCCGAACTAAAATGTGGTGACCTGGAAGAAGAACTCAAGAATGTCACTAACAACCTGAAGT
CACTAGAGGCTGCATCTGAAAAGTATTCTGAAAAGGAGGACAAATACGAAGAAATTAAACTTCTCTCCGGCAAACTGAAA
GAGGCTGAGACCCGTGCCAAATTTGCAGAGAGAACAGTTGCAAAACTGGAAAAGACAATTGATGACCTGGAAGAAAAACT
GGCCCAGGCCAAAGAAGAGAATGTGGGCTTACATCAGACACTGGATCAGACACTAAACGAACTAAACTGTATA

Alignment

ORF - retro_btau_1604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 84.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQKKLKETEDELDKYSENLKDAQEKLE-LTEKKASDAEGDVAALNRRIQLVEEELDRAQERLATALQKLE
          ...K........D.........Q..L..........AEGDVAALNR.IQLVEEELDRAQER.ATALQKL.
Retrocopy VKRKIQALQQQADEAEDRAQGLQRELD<RQGERREKAEGDVAALNRCIQLVEEELDRAQERPATALQKLK

Parental  EAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAE
          EAEKAADESERGMKVI.NRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEE.AE
Retrocopy EAEKAADESERGMKVIGNRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEECAE

Parental  VSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTVAKLEKTID
          VSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKY.EEIKLLS.KLKEAETRA.FAERTVAKLEKTID
Retrocopy VSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKY-EEIKLLSGKLKEAETRAKFAERTVAKLEKTID

Parental  DLEEKLAQAKEENVGLHQTLDQTLNELNCI
          DLEEKLAQAKEENVGLHQTLDQTLNELNCI
Retrocopy DLEEKLAQAKEENVGLHQTLDQTLNELNCI

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
ERP005899_liver	0.00 RPM	69.86 RPM
ERP005899_muscle	0.37 RPM	190.25 RPM
SRP017611_brain	0.18 RPM	40.70 RPM
SRP017611_kidney	0.36 RPM	207.51 RPM
SRP017611_liver	0.00 RPM	33.98 RPM
SRP030211_testis	0.02 RPM	22.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1604 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604 , retro_btau_1758,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
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,