RetrogeneDB ID: retro_btau_409

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:60015901..60016196(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSBTAG00000019701
• Aliases: None
• Description: 60S ribosomal protein L31 [Source:UniProtKB/Swiss-Prot;Acc:Q56JX3]

Sequence

>retro_btau_409
TTAGTGATGAGAAAATATACCATCAACATTCATGAGTGCATCCATAGAGTGAGCATCAAGAAGTGTGCCCCTCAGGCACT
CAAAGAGATCCAGAAATTTGCCATTTAAGGAGACAGAATGTCCAGATGTGCCCATTGACACTGGGCTCAACAAAGCATTA
AGGGCTAAAGGAGTAAGAACTGTCCCATACTGTATCTGTGTGTGGTTATCCAGAAAACACAATGAGGATGAAGATTCCAT
AAACAAACTAAATACATTGGTTACTCAGGTACTTGTCATCATTTCCAAAACTTTA

Alignment

ORF - retro_btau_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.66 %
• Parental protein coverage: 78.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAM-KEMGTPDVRIDTRLNKAVWAKGIRNVPYRIRVRL
          .V.R.YTINIH..IH.V..KK.AP.ALKEI.KFA..KE...PDV.IDT.LNKA..AKG.R.VPY.I.V.L
Retrocopy LVMRKYTINIHECIHRVSIKKCAPQALKEIQKFAI>KETECPDVPIDTGLNKALRAKGVRTVPYCICVWL

Parental  SRKRNEDEDSPNKLYTLVTYVPVTTFKNL
          SRK.NEDEDS.NKL.TLVT.V.V...K.L
Retrocopy SRKHNEDEDSINKLNTLVTQVLVIISKTL

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	0.07 RPM	115.35 RPM
ERP005899_muscle	0.11 RPM	1167.11 RPM
SRP017611_brain	0.00 RPM	110.00 RPM
SRP017611_kidney	0.06 RPM	171.06 RPM
SRP017611_liver	0.00 RPM	89.25 RPM
SRP030211_testis	0.09 RPM	139.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_409 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_409 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 161 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Bos taurus	ENSBTAG00000019701	9 retrocopies	retro_btau_1043, retro_btau_1100, retro_btau_1553, retro_btau_160, retro_btau_1777, retro_btau_1783, retro_btau_409 , retro_btau_524, retro_btau_867,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Microcebus murinus	ENSMICG00000016059	15 retrocopies	retro_mmur_1018, retro_mmur_1028, retro_mmur_1080, retro_mmur_130, retro_mmur_1320, retro_mmur_1369, retro_mmur_1386, retro_mmur_1606, retro_mmur_1617, retro_mmur_476, retro_mmur_506, retro_mmur_538, retro_mmur_639, retro_mmur_796, retro_mmur_996,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Mus musculus	ENSMUSG00000073702	41 retrocopies	retro_mmus_1054, retro_mmus_1143, retro_mmus_1256, retro_mmus_1419, retro_mmus_1456, retro_mmus_1495, retro_mmus_1507, retro_mmus_1532, retro_mmus_1598, retro_mmus_1670, retro_mmus_1674, retro_mmus_1768, retro_mmus_1823, retro_mmus_1836, retro_mmus_1856, retro_mmus_2054, retro_mmus_2152, retro_mmus_2240, retro_mmus_2278, retro_mmus_2398, retro_mmus_2554, retro_mmus_2603, retro_mmus_2620, retro_mmus_2630, retro_mmus_2658, retro_mmus_2677, retro_mmus_2716, retro_mmus_2821, retro_mmus_2959, retro_mmus_2966, retro_mmus_3186, retro_mmus_3196, retro_mmus_3380, retro_mmus_367, retro_mmus_396, retro_mmus_446, retro_mmus_453, retro_mmus_485, retro_mmus_592, retro_mmus_933, retro_mmus_964,
Oryctolagus cuniculus	ENSOCUG00000002392	9 retrocopies	retro_ocun_1070, retro_ocun_1074, retro_ocun_1161, retro_ocun_117, retro_ocun_1366, retro_ocun_206, retro_ocun_64, retro_ocun_941, retro_ocun_99,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,
Ictidomys tridecemlineatus	ENSSTOG00000010902	15 retrocopies	retro_itri_1068, retro_itri_1074, retro_itri_1077, retro_itri_1140, retro_itri_1142, retro_itri_1223, retro_itri_1467, retro_itri_1570, retro_itri_1634, retro_itri_1791, retro_itri_1900, retro_itri_298, retro_itri_450, retro_itri_680, retro_itri_76,
Tarsius syrichta	ENSTSYG00000005427	33 retrocopies	retro_tsyr_1102, retro_tsyr_117, retro_tsyr_1211, retro_tsyr_1535, retro_tsyr_1610, retro_tsyr_1692, retro_tsyr_1861, retro_tsyr_1912, retro_tsyr_1947, retro_tsyr_2001, retro_tsyr_2026, retro_tsyr_2030, retro_tsyr_2079, retro_tsyr_2089, retro_tsyr_2092, retro_tsyr_2100, retro_tsyr_2105, retro_tsyr_2162, retro_tsyr_239, retro_tsyr_294, retro_tsyr_485, retro_tsyr_551, retro_tsyr_596, retro_tsyr_617, retro_tsyr_635, retro_tsyr_666, retro_tsyr_712, retro_tsyr_754, retro_tsyr_766, retro_tsyr_780, retro_tsyr_785, retro_tsyr_813, retro_tsyr_909,