RetrogeneDB ID: retro_btau_226

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:35698744..35700058(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000013700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSBTAG00000019914
• Aliases: BECN1, ATG6
• Description: Beclin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q4A1L4]

Sequence

>retro_btau_226
AGAGTCAAGGCCTCCACCATGTCCCACTTCTGCTTTCTTTGCCAGCGCTGCAGCCAGGCTCTGAAGCTGAATCACTCTGT
GGAGCCCTCCCAGGAACCTGGAGCTTCGATGCTCATCTCAGCTCAGGGAGAGACAAGAGAAACACCGGAGGGAGGCCCTC
CCTCCAAGGAGGAGGCAAACTTTGAAAATCTACAGGATGGCGCCTTTTGCAGGACTCCTCACCCCCCCAGTGGTGGGATG
TCCTGGGACTATTCCAGCTTCACCCTGCTTGGGAGGTTGGAGCCCTGGAGGAGTCTCAACAGCATCCAGAAGACTATTAG
GGACAGTTCTGACATCCTCTCTGGTGAAACAGAGGTGGACCACCCGCTGTGTGTGGACTGTACTGACTATCTTTTAGAGG
TACTGGACGTTGAACTCGCCATCACAGAATCTGACGTTCAGAACTACAAACGCTGTTTGGAGACCAGGAAGTGGTTGAGT
GGGGACGACAGGGAGATGCTGCAGGAGAAGCTGAAGGGCCTGGAGTTGGAGGAAGCGAGGCTACTCCAGGAAGTGGCAGA
AGTGGAAAAGAACCAAGAAAGGGTAGCAGCCGATCTTGAGGCAGCCCAGGCAGAGACGAAGATGCTGGAGCAGCAGGAAA
AGCAGTACTGGGAGGACTACAGTCAACTGAAATGGCAACAATTAGAACTAAATGAGGAGCTGAGCAGTGTGGAGATGCGA
CTGCAGTACGCCCAGCTCCAGTGCAACCAGTTGGAGAAAACCGACGTCTTTAATGCCACCTTCGAGATCTGGCAAGACGG
CCCCTTACCCGTCATCAATAACTTCAGACTGGGCCGCCTCCCTACTGTCCCTGTGTGCTGGGATGAGATCAGTGCAGCCT
GGGGACAGACAGCCTTGCTGCTCCTCGCCCTGGCCAATACAGTTGGACTGGAGTTTCAGAGGTACCATCTCATCCCCTGC
GGAAGCCATTCCTACCTGAGGTCTTTAATAGATGATTGTGCCGAGTTGCCATTGTTCTCTAGTGGGAAGCAGAATGTTTT
CTTACATAACAAATTTGATCAGGCTATGATGGCTTTCCTGGACTGCATGCAGCAGTTCAAGGAAGCAGCTGAGAGCGGTG
AGTCGGGTCTCTGTTTGCCCTACAAGATTCATGTGAAGAAAGGCCTGATGGAAGACCCTGGAAGCAGCAGTGGATTCTAT
TCCATCAGAACCCACTTGAACACGGAGGAGGACTGGACGAAGGCGCTCAAGCTCATGCTTATCAATTTTAAGTGTAGTCT
CACTTGGGTCTCCTTAAGGTATGGTCGAAAATAA

Alignment

ORF - retro_btau_226 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.93 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QELTAPLLATAQLKPGETQEEEANSGEEPFIETRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTME
          QE..A..L..AQ....ET.E....S.EE...E..QDG...R...P..........SFTL.G.........
Retrocopy QEPGASMLISAQGETRETPEGGPPSKEEANFENLQDGAFCRTPHPPSGGMSWDYSSFTLLGRLEPWRSLN

Parental  NLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
          ..........D..DI.SG.T.VDHPLC..CTD.LL..LD..L..TE...QNYKRCLE.......DD.E.L
Retrocopy SIQKTIR---DSSDILSGETEVDHPLCVDCTDYLLEVLDVELAITESDVQNYKRCLETRKWLSGDDREML

Parental  GLELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSV
          ...LK.L.LEE.RL.QE...VEKN...VA..LE..QAE...L.Q.E.QY...YS..K.QQLEL..EL.SV
Retrocopy QEKLKGLELEEARLLQEVAEVEKNQERVAADLEAAQAETKMLEQQEKQYWEDYSQLKWQQLELNEELSSV

Parental  ENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANK
          E....YAQ.Q...L.KT.VFNATF.IW..G....INNFRLGRLP.VPV.W.EI.AAWGQT.LLL.ALAN.
Retrocopy EMRLQYAQLQCNQLEKTDVFNATFEIWQDGPLPVINNFRLGRLPTVPVCWDEISAAWGQTALLLLALANT

Parental  MGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRF
          .GL.FQRY.L.P.G.HSYL.SL.D...ELPL..SG....F..NKFD.AM.AFLDC.QQFKE..E.GE...
Retrocopy VGLEFQRYHLIPCGSHSYLRSLIDDCAELPLFSSGKQNVFLHNKFDQAMMAFLDCMQQFKEAAESGESGL

Parental  CLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK
          CLPY...V.KG..ED.G.S.G.YSI.T..N.EE.WTKALK.ML.N.K..L.WVS.....K
Retrocopy CLPYKIHVKKGLMEDPGSSSGFYSIRTHLNTEEDWTKALKLMLINFKCSLTWVSLRYGRK

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	15.43 RPM
ERP005899_muscle	0.11 RPM	54.21 RPM
SRP017611_brain	0.27 RPM	52.81 RPM
SRP017611_kidney	0.06 RPM	59.33 RPM
SRP017611_liver	0.00 RPM	29.07 RPM
SRP030211_testis	0.06 RPM	65.35 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_226 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_226 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226 ,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,