RetrogeneDB ID: retro_ttru_1316

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110312:102716..103421(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000001515
• Aliases: None
• Description: None

Sequence

>retro_ttru_1316
CAGGCTGGGCCAGTAATAAAAGTGAAAATTCCAAAAGATAAGGATGGTAAACCAAAGCAGTTTGCGTTTGTGAATTTCAA
ACGTGAAGTTATCTGTTCCTTATGCCATGAATCTGCTTAACGGAATCAAACTTTTTGGAAGGCCCATCAAACTTCAGTTT
AGATCAGGAAGCAGCCATGCCTCACAGGAGGTCAGTTTGTCATATTCCCAGCAGCATGTTGGAAGTTCAAGCCCTACTTC
CACGTCTCCTAGCAGGTACGAAAGGACAGTGGATAACATGACTCCATCAACACCGATAATTCAAAGATCTTTTTCTTCTT
CAGAAAATTTTCAGAGACAAGCAGTGATGAACAGTGCTTTGAGACAGATGTCCTATGGAGGGAAATTTGGTTCTCCACAT
CTGGATCAATCAGGATTTTCCCCATCAGCTCAGTCACATAATCATACTTTTAACCAGTCTTCAACCTCCCAGTGGGGCCA
AGATACACCATTATCACAGCGAAAAGTCGGACAGAATTCTCGTCCTTACGTAGTGGATAGACATAGCCGTGAACAGTATT
ACACTGACCATGGGTCCAACCATCATTACAGAGGAAGCAGAGATGATTTCTTCTATGAAGAGAGAAATCACTTCATGGCT
GGAGCCATGACTATGATAACAGAAGAGACAGTGGTAGCGATGGAAATTGGCACTCATCTCGACAC

Alignment

ORF - retro_ttru_1316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.87 %
• Parental protein coverage: 88.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAGPVIKVKIPKDKDGKPKQFAFVNFKHEV-SVPYAMNLLNGIKLFGRPIKIQFRSGSSHASQEVSSSYP
          QAGPVIKVKIPKDKDGKPKQFAFVNFK.EV.SVPYAMNLLNGIKLFGRPIK.QFRSGSSHASQEVS.SY.
Retrocopy QAGPVIKVKIPKDKDGKPKQFAFVNFKREV>SVPYAMNLLNGIKLFGRPIKLQFRSGSSHASQEVSLSYS

Parental  QHHVGSSSPTSTSPSSRYERTVDNMTPSTPIIQRSFSSSENFQRQAVMNSVLRQMSYGGKFGSPHLDQSG
          Q.HVGSSSPTSTSPS.RYERTVDNMTPSTPIIQRSFSSSENFQRQAVMNS.LRQMSYGGKFGSPHLDQSG
Retrocopy QQHVGSSSPTSTSPS-RYERTVDNMTPSTPIIQRSFSSSENFQRQAVMNSALRQMSYGGKFGSPHLDQSG

Parental  FSPSVQSHNHTFNRSSTSQWRQDTPLSQRKVRQNSHTYAVDRHYSREQRYTDHGSDHHYRGSRDD-FFYE
          FSPS.QSHNHTFN.SSTSQW.QDTPLSQRKV.QNS..Y.VDRH.SREQ.YTDHGS.HHYRGSRDD.F..E
Retrocopy FSPSAQSHNHTFNQSSTSQWGQDTPLSQRKVGQNSRPYVVDRH-SREQYYTDHGSNHHYRGSRDDFFYEE

Parental  -ERNPDGWSHDYDNRRDSGRDGKWRSSRH
          .E....GWSHDYDNRRDSG.DG.W.SSRH
Retrocopy <EKSLHGWSHDYDNRRDSGSDGNWHSSRH

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_1316 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1316 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316 , retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,