RetrogeneDB ID: retro_btau_1334

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:105475702..105476197(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.85322
• Ensembl ID: ENSBTAG00000015598
• Aliases: None
• Description: 40S ribosomal protein S10 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0F4]

Sequence

>retro_btau_1334
ATGTTGATGCCCAAGAAGAACTGGATTGCCATTTATGAACTCCTTTTTAAGGAGGGGGTGATGATGGCCAAGAAGGATGT
CCACATGCCCAAGCACCTGGAGCTAGCAGACAAGAATGTGCCCAATCTTCACGTCATGGAAGCCATGCAGTCTCTCAAGT
CACGAGGCTACGTGAAGGAACAGTTTGCCTGAAGACATTTCTACTGGTACCTCACCAACGAAGGCATCCAGTATCTCTGT
GATTGCCCCCACCTGCCCCCTGAGATCGTGCCCACCACCCTGCGCCGCAGCCGTCCTGAGACTGGCCGGCCAAGGCCCAA
AGGTCTGCAGGGAGAGCGGCCTGCAAGACTCATGCGAGGGGAAGCCGACAGAGACATCTACAGACGAAGCGCCGTGCCCC
CTGGTGCCGACAAGAAAGCCAAGGCCGGGGCTGGGTAGGCAACTGAATTCCAGTTTAGAGGTGGATTTGGCCGTGGACGT
GGTCAGCCACCTCAG

Alignment

ORF - retro_btau_1334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
          MLMPKKN.IAIYELLFKEGVM.AKKDVHMPKH.ELADKNVPNLHVM.AMQSLKSRGYVKEQFA.RHFYWY
Retrocopy MLMPKKNWIAIYELLFKEGVMMAKKDVHMPKHLELADKNVPNLHVMEAMQSLKSRGYVKEQFA*RHFYWY

Parental  LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKA
          LTNEGIQYL.D..HLPPEIVP.TLRRSRPETGRPRPKGL.GERPARL.RGEADRD.YRRSAVPPGADKKA
Retrocopy LTNEGIQYLCDCPHLPPEIVPTTLRRSRPETGRPRPKGLQGERPARLMRGEADRDIYRRSAVPPGADKKA

Parental  EAGAGSATEFQFRGGFGRGRGQPPQ
          .AGAG.ATEFQFRGGFGRGRGQPPQ
Retrocopy KAGAG*ATEFQFRGGFGRGRGQPPQ

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	104.90 RPM
ERP005899_muscle	0.53 RPM	1011.07 RPM
SRP017611_brain	0.00 RPM	121.69 RPM
SRP017611_kidney	0.06 RPM	171.47 RPM
SRP017611_liver	0.08 RPM	151.32 RPM
SRP030211_testis	0.07 RPM	141.93 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1334 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1334 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015598	3 retrocopies	retro_btau_1334 , retro_btau_844, retro_btau_989,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Myotis lucifugus	ENSMLUG00000007495	2 retrocopies	retro_mluc_1143, retro_mluc_2128,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,