RetrogeneDB ID: retro_btau_235

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:2084727..2085246(-)
• Located in intron of: ENSBTAG00000002303

Retrocopy information

• Ensembl ID: ENSBTAG00000004526
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSBTAG00000010156
• Aliases: TPT1, TCTP
• Description: Translationally-controlled tumor protein [Source:UniProtKB/Swiss-Prot;Acc:Q5E984]

Sequence

>retro_btau_235
ATGATCATCTACCGGGACCTCATTAGCCATGACAAGATGTTCTCCGACATCTACAAGATCCGGGAGGTCGCAGACGGGCT
GTGTCTGGAGGTGGAGGGGAAGATGGTCAGTAGGACAGAGGGTAACATCGATGACTCACTCATTGGTGGAAATGCCTCCG
CTGAAGGCCCCGATGGCGAAGGTACCGAAAGCACAGTAATCACTGGTGTCGATATTGTCATGAACCATCGCTTGCAGGAA
ACCAGCTTCACAAAAGAAGCCTACAAGAAGTACATCAAAGATTACATGAAGTCAATCAAAGGGAAACTTGAAGAACAGAG
ACCAGAAAGAGTAAAACCTTTTATGACAGGGGCTGCAGAACAAATCAAGCACATCCTTGCTAATTTCAAAAACTATCAGT
TCTTTATTGGTGAAAACATGAATCCAGATGGCATGGTTGCTCTGCTGGACTACCGTGAGGATGGTGTAACCCCATATATG
ATTTTCTTTAAGGATGGTTTAGAGATGGAAACATGTTAA

Alignment

ORF - retro_btau_235 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIIYRDLISHDEMFSDIYKIREVADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGV
          MIIYRDLISHD.MFSDIYKIREVADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGP.GEGTESTVITGV
Retrocopy MIIYRDLISHDKMFSDIYKIREVADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPDGEGTESTVITGV

Parental  DIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENM
          DIVMNH.LQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENM
Retrocopy DIVMNHRLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENM

Parental  NPDGMVALLDYREDGVTPYMIFFKDGLEMEKC
          NPDGMVALLDYREDGVTPYMIFFKDGLEME.C
Retrocopy NPDGMVALLDYREDGVTPYMIFFKDGLEMETC

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	0.58 RPM	528.97 RPM
ERP005899_muscle	1.95 RPM	3725.91 RPM
SRP017611_brain	0.18 RPM	246.35 RPM
SRP017611_kidney	0.71 RPM	885.99 RPM
SRP017611_liver	0.45 RPM	686.37 RPM
SRP030211_testis	0.14 RPM	202.36 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_235 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 115 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Bos taurus	ENSBTAG00000010156	2 retrocopies	retro_btau_21, retro_btau_235 ,
Callithrix jacchus	ENSCJAG00000019229	2 retrocopies	retro_cjac_1786, retro_cjac_314,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Loxodonta africana	ENSLAFG00000021740	7 retrocopies	retro_lafr_1008, retro_lafr_1195, retro_lafr_1211, retro_lafr_1247, retro_lafr_347, retro_lafr_484, retro_lafr_883,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Nomascus leucogenys	ENSNLEG00000002108	8 retrocopies	retro_nleu_1262, retro_nleu_1281, retro_nleu_1637, retro_nleu_2127, retro_nleu_2539, retro_nleu_2540, retro_nleu_368, retro_nleu_9,
Otolemur garnettii	ENSOGAG00000012523	20 retrocopies	retro_ogar_1141, retro_ogar_1249, retro_ogar_1538, retro_ogar_1682, retro_ogar_1754, retro_ogar_2193, retro_ogar_2225, retro_ogar_2298, retro_ogar_2331, retro_ogar_2594, retro_ogar_2668, retro_ogar_2819, retro_ogar_2893, retro_ogar_2944, retro_ogar_344, retro_ogar_350, retro_ogar_3503, retro_ogar_622, retro_ogar_746, retro_ogar_906,
Procavia capensis	ENSPCAG00000016228	3 retrocopies	retro_pcap_245, retro_pcap_351, retro_pcap_357,
Sorex araneus	ENSSARG00000009319	1 retrocopy	retro_sara_113,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,
Tupaia belangeri	ENSTBEG00000013539	25 retrocopies	retro_tbel_1009, retro_tbel_1556, retro_tbel_1634, retro_tbel_1724, retro_tbel_1725, retro_tbel_2086, retro_tbel_2100, retro_tbel_2265, retro_tbel_2278, retro_tbel_2464, retro_tbel_2550, retro_tbel_2767, retro_tbel_3238, retro_tbel_3354, retro_tbel_3403, retro_tbel_3410, retro_tbel_3592, retro_tbel_3888, retro_tbel_4226, retro_tbel_4400, retro_tbel_4526, retro_tbel_459, retro_tbel_4641, retro_tbel_4733, retro_tbel_830,
Tarsius syrichta	ENSTSYG00000003160	13 retrocopies	retro_tsyr_1054, retro_tsyr_1291, retro_tsyr_1549, retro_tsyr_1601, retro_tsyr_2120, retro_tsyr_314, retro_tsyr_655, retro_tsyr_763, retro_tsyr_781, retro_tsyr_784, retro_tsyr_890, retro_tsyr_958, retro_tsyr_990,
Vicugna pacos	ENSVPAG00000008472	5 retrocopies	retro_vpac_1, retro_vpac_101, retro_vpac_159, retro_vpac_539, retro_vpac_552,