RetrogeneDB ID: retro_ttru_1401

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112419:4746..5965(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSTTRG00000007597
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_ttru_1401
ATGCTGGTCACCCTGGAGACCGTCCAGCAGCAGATCTTCAAGATCGACATCGACCCAAACGAGATGGTAAGAGCACTGAA
TGAGAAGACTGAATCTGAAAAGGGTAAAGATGCCTTTCCTGTAGCAGGTCAAAAATTAATTTAGCAGGCAAAATTCTCAA
TAATGATACTGCTCTAAAAGAATATAAAATTGACGAGAAAAACTTCGTGGTAGTTATGGTGAGAAGACCCAAAGCAGTGA
CACCACCAGCACCAGCTACAACTTAGCAATCTAATTCTGCCACCACTACCACAGTTAGTTCCTCCACAGCACCAGCTGTG
GCTCAGGCCCCAACCCCTGCCCTCACTTTGGCCCCCACTCCCACACCTGCATCTGTCACTCCAGCATCAACGACAGCATC
TTCTGAACCTGCACCTGCTAGTGCAATGAAACAAGAAAAACCTGCAGAAAAGCCAGCAGAAACACCAGTGGCTGCTAGCC
CAACATCAACTGACAGTACATCAGGTGATTCTTCTTGGTCAAACCTTTTTGAAGATGCAACAAGTGCCCTTGTGACAAGT
CAGTCTTAGGAGAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGGCAGCAAGTAATCGCAGCACTGAGAGCCAG
TTTCAACAACCCTGACAGCAGTGGAGTATTTTTTAATGGGAATTCCCAGAGATAGAGAAAGTCAGGCCGTGGTTGACTCC
CCTCCAGCAGCGAGTAGTGGGGCTCCTCAGTCTTCAGTGGCTGCAGCTGCAGCAACTACGACAGCAACAACTACAACAAG
TTCTGGAGCACACCCTCTTGCATTTTTACGGAATCAGCCTCAGTTTCAACAGAGGAGACAAATTATTCAACAGAATCCTT
CCCTGCTTCCAGCATCGCTACAACAGATAGGTCGAGAAAATCCTCAGTTACTGCAGCAAATTAGCCACCATCAGGAGCAT
TTTATTCAGATGTTATATTGAACCAGTTCAAGAAGTGGGGGGTCAAGGAGGAGGGGGTGGAAGTGGCAGTGGAGGAATTG
CAGAAGCTGGAAGTGGTCATATGAACTACATTCAAATAACGCCTCAGGAAGAAGAAGCTATAGAAAGGTTAAAGGCATTA
GGATTTCCTGAAGGACTTGTGATACAAGCATATTTTGCTTGTGAGAGGAATGAGAACTTGGCTGCCAATTTTCCTGTACA
GCAAAACTTTGATGAAGAT

Alignment

ORF - retro_ttru_1401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLVTL-TLQQQTFXXXXXXXXXVRALKEKIESEKGKDAFPVAGQKLI-YAGKILNDDTALKEYKIDEKNF
          MLVTL.T.QQQ.F.........VRAL.EK.ESEKGKDAFPVAGQKLI..AGKILN.DTALKEYKIDEKNF
Retrocopy MLVTLETVQQQIFKIDIDPNEMVRALNEKTESEKGKDAFPVAGQKLI<LAGKILNNDTALKEYKIDEKNF

Parental  VVVMVTKPKAVTTPAPATTQQSNSATTTTVSSSTAPTVVQAPTPAPTLAPAPAPTPASVTPASTTASSEP
          VVVMV..PKAVT.PAPATT.QSNSATTTTVSSSTAP.V.QAPTPA.TLAP.P..TPASVTPASTTASSEP
Retrocopy VVVMVRRPKAVTPPAPATT*QSNSATTTTVSSSTAPAVAQAPTPALTLAPTP--TPASVTPASTTASSEP

Parental  APASATKQEKPAEKPAETPVAASPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQV
          APASA.KQEKPAEKPAETPVAASPTSTDSTSGDSS.SNLFEDATSALVT.QS.ENMVTEIMSMGYER.QV
Retrocopy APASAMKQEKPAEKPAETPVAASPTSTDSTSGDSSWSNLFEDATSALVTSQS*ENMVTEIMSMGYERQQV

Parental  IAALRAS-FNNPDR-AVEYLLMGIPGDRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPL
          IAALRAS.F..P...AVEY.LMGIP.DRESQAVVD.PPAAS.GAPQSSVAAAAATTTATTTT.SSG.HPL
Retrocopy IAALRAS<FQQP*Q<AVEYFLMGIPRDRESQAVVDSPPAASSGAPQSSVAAAAATTTATTTT-SSGAHPL

Parental  EFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLN-EPVQEAGGQGGGSGGG
          .FLRNQPQFQQ.RQIIQQNPSLLPA.LQQIGRENPQLLQQIS.HQEHFIQML..EPVQE.GGQGGG.G.G
Retrocopy AFLRNQPQFQQRRQIIQQNPSLLPASLQQIGRENPQLLQQISHHQEHFIQMLY>EPVQEVGGQGGGGGSG

Parental  SGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          SGGIAEAGSGHMNYIQ.TPQE.EAIERLKALGFPEGLVIQAYFACE.NENLAANF..QQNFDED
Retrocopy SGGIAEAGSGHMNYIQITPQEEEAIERLKALGFPEGLVIQAYFACERNENLAANFPVQQNFDED

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_1401 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1401 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401 ,