RetrogeneDB ID: retro_btau_417

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:4648057..4648363(-)
• Located in intron of: ENSBTAG00000012449

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSBTAG00000001521
• Aliases: None
• Description: Cytochrome b-c1 complex subunit 7 [Source:UniProtKB/Swiss-Prot;Acc:P00129]

Sequence

>retro_btau_417
GTCAAAACATCAGGCAGATGACTGGAGGGTATTCGAAGATGGTATTGCAGCGCTGTTGGGTTCATTACCCTGGGCTGACT
CTGAGGTGACGCGGTATATGAGAATGACGATGTAAGAGAAGCCACAAGAAGGCTTCCTGAGAGCTTTTGTAATGACAGGG
GGTACATATTAGGAGAGCGCTGGACCTGAGCATGAAGAAACAGGTTTTGCCTTTAGATCAGTGGACAAAATATGAGGAGG
ATAAATTCTACCTTGAACCATACCCTGAAAGAGGGTATTTGGGAAAGAAAAGAGAGAGAAGAATTC

Alignment

ORF - retro_btau_417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.42 %
• Parental protein coverage: 91.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSASSRWLEGIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYNDRVF-RIKRALDLSMRQQI
          V..S.R.LEGIR.WY..A.GF..LG....D...ENDDV.EA.RRLPE...NDR....I.RALDLSM..Q.
Retrocopy VKTSGR*LEGIRRWYCSAVGFITLG*L*GDAVYENDDVREATRRLPESFCNDRGY<HIRRALDLSMKKQV

Parental  LPKEQWTKYEEDKSYLEPY-LKEVIRERKEREEW
          LP..QWTKYEEDK.YLEPY.LKE.I.ERKEREE.
Retrocopy LPLDQWTKYEEDKFYLEPY>LKEGIWERKEREEF

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	34.82 RPM
ERP005899_muscle	0.00 RPM	52.47 RPM
SRP017611_brain	0.00 RPM	28.14 RPM
SRP017611_kidney	0.00 RPM	75.99 RPM
SRP017611_liver	0.00 RPM	23.63 RPM
SRP030211_testis	0.00 RPM	52.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_417 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_417 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001521	3 retrocopies	retro_btau_1641, retro_btau_374, retro_btau_417 ,
Choloepus hoffmanni	ENSCHOG00000007884	22 retrocopies	retro_chof_1256, retro_chof_1271, retro_chof_1468, retro_chof_1662, retro_chof_1888, retro_chof_2017, retro_chof_2170, retro_chof_2332, retro_chof_2528, retro_chof_2536, retro_chof_2554, retro_chof_257, retro_chof_2684, retro_chof_394, retro_chof_524, retro_chof_599, retro_chof_635, retro_chof_654, retro_chof_699, retro_chof_766, retro_chof_773, retro_chof_975,
Equus caballus	ENSECAG00000009780	1 retrocopy	retro_ecab_1116,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Pteropus vampyrus	ENSPVAG00000012321	1 retrocopy	retro_pvam_498,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tupaia belangeri	ENSTBEG00000002453	28 retrocopies	retro_tbel_1046, retro_tbel_1268, retro_tbel_1357, retro_tbel_1568, retro_tbel_1583, retro_tbel_1656, retro_tbel_1688, retro_tbel_169, retro_tbel_1858, retro_tbel_2106, retro_tbel_2217, retro_tbel_248, retro_tbel_2675, retro_tbel_274, retro_tbel_2883, retro_tbel_2885, retro_tbel_2893, retro_tbel_2942, retro_tbel_3129, retro_tbel_3156, retro_tbel_3291, retro_tbel_3492, retro_tbel_3662, retro_tbel_4334, retro_tbel_4539, retro_tbel_457, retro_tbel_517, retro_tbel_784,
Tursiops truncatus	ENSTTRG00000007348	3 retrocopies	retro_ttru_1106, retro_ttru_501, retro_ttru_754,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,