RetrogeneDB ID: retro_ttru_595

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2812:113487..114717(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000014255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSTTRG00000011716
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_ttru_595
ACCTCCCAAGAACCTGAAGCTTTGATGCTCATCCCAGCTCAGGGGGAGCCAGGAAAAACCCAGGAGGGAGACCCTCCTTC
CAGGGAGGAGGCAGATTTTGAAAATCTACAGGAAGGTGCCTCGTACAGGACCCTTCCTGGCCTCCCTGGTGGCAGAACGT
CCTGGGACAATCCTGACAGCTTCACCCTGCTTGGGAATTTGGGCTCCCTGAGAACTCTCAGTAACATCCAGAAGGCTGCA
AGCGACATGTTTGACATCCTCTCTGGTGAAACAGATGTGGACCACCCCATGTGTGAGGACTGTACTGACAATCTTTTAGA
GCAACTGGACGTCCAACTCACCATCACAGAATCTGAGATTCAGAGCTACAAACGCTGTTTGGAGACCAGGGAGTTGATAA
GTGAGGAGAGGGAGTCGCTGCAGGAGAAGCTGAAGGGCCTGGAGCTGGAGGAAACGAGGCTGGTCCAGGAGCTGGAGGAG
GTGGAAAAGAACCGAGAAAGAGCAGCAGCAGATCTCGAGGCAGCCCAGGCAGAGACTGAGATGCTGGACCAGCAAGAAAA
GCAGTACCAGAAGGACTACAGTAAATTGAAATGGCAACAACTAGAACTACATGACGAGCTGAGTAGTGTGGAGAAGCGGC
TATGGTACGCCCAGATCCAGTGGCACCAGCTGGAGAAAACCAGTATCTTTAATGCCACATTTGAGATCTGGCATGATGGC
CCCTTAACTACCATCAATAACTTCAGATTGGGCTGCCTCCCCACTGTCCCTGTGTGCTGGAATGAGATTAACATAGCCTG
GGGACAGACAGCCTTGCTGCTCCTTGCCCTGTCCAATACAATTGGACTGGAGTTTCAGAGGTACCGACTCATCCCCTGTG
GAAACCATTCCTATCTGAAGTCTTTAACAGATGACTGCATTGAGCTGCCATTGTTCTCTAATGGGAAGCGGAATGTTTTC
TTGCATAACAAATTTGACCAGGCTATGATGGCTTTCCTGGACTGCATGCAGCAGTTCAAGGAACTGGCTGAGAAAGGTGG
GTCAGGTCTCTGCTTGCCCTACAAGATTCATGTGAAGAAAGGCCTGATGGAAGACCCCGGAAGCAGTGGTGGATTCTACT
CCATCAGAACCCACTTGAACACAGAGGAGGAGTGGACAAAAGCACTCAAGCTTATGCTTATAAATTTTGAGTGTAGTCTC
ACTTGGGTCTCCTTAAGATATTGTCAAAAA

Alignment

ORF - retro_ttru_595 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.73 %
• Parental protein coverage: 91.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIQELTAPLLATAQVKPGETQEEEANSGEEPFIETRQDGVSRRFIP--PARMMSTESANSFTLIGEASDG
          T.QE..A..L..AQ..PG.TQE....S.EE...E..Q.G.S.R..P..P....S.....SFTL.G.....
Retrocopy TSQEPEALMLIPAQGEPGKTQEGDPPSREEADFENLQEGASYRTLPGLPGGRTSWDNPDSFTLLGNL---

Parental  GTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDD
          G....LS...K...D.FDI.SG.TDVDHP.CE.CTD.LL.QLD.QL..TE.E.Q.YKRCLE..E...E..
Retrocopy GSLRTLSNIQKAASDMFDILSGETDVDHPMCEDCTDNLLEQLDVQLTITESEIQSYKRCLETRELISEE-

Parental  SEQLQMELKELALEEERLIQELEDVEKNRQIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDE
          .E.LQ..LK.L.LEE.RL.QELE.VEKNR...A..LE..QAE.E.LDQ.E.QYQ..YS..K.QQLEL.DE
Retrocopy RESLQEKLKGLELEETRLVQELEEVEKNRERAAADLEAAQAETEMLDQQEKQYQKDYSKLKWQQLELHDE

Parental  LKSVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHA
          L.SVE....YAQ.Q...L.KT..FNATF.IWH.G...TINNFRLG.LP.VPV.WNEIN.AWGQT.LLL.A
Retrocopy LSSVEKRLWYAQIQWHQLEKTSIFNATFEIWHDGPLTTINNFRLGCLPTVPVCWNEINIAWGQTALLLLA

Parental  LANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKG
          L.N..GL.FQRYRL.P.GNHSYL.SLTD...ELPL...G....F..NKFD.AM.AFLDC.QQFKE..EKG
Retrocopy LSNTIGLEFQRYRLIPCGNHSYLKSLTDDCIELPLFSNGKRNVFLHNKFDQAMMAFLDCMQQFKELAEKG

Parental  ETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK
          ....CLPY...V.KG..ED.G.SGG.YSI.T..N.EE.WTKALK.ML.N....L.WVS.....K
Retrocopy GSGLCLPYKIHVKKGLMEDPGSSGGFYSIRTHLNTEEEWTKALKLMLINFECSLTWVSLRYCQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_595 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_595 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,