RetrogeneDB ID: retro_ttru_1030

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100459:33562..33913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB2
• Ensembl ID: ENSTTRG00000015454
• Aliases: None
• Description: transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) [Source:HGNC Symbol;Acc:11619]

Sequence

>retro_ttru_1030
ATAGACGTGTTCCTCATGATCCGGCGCCACAAGACCACCATCTTCATGGACGCCAAGAAATCGAGCACCGTGTGCGAGCT
GAAGTGCATTGTCGAGGGCATCCTCAAGTGGCCGCTGGTGGAGCAGTGGCTGTACAAGGACGACCAGCTTCTGGACGACA
GAAAGACATTGGGCGAGTGTGGCTTCACCAGCCAGACAGCATGGCCTCGGGCCCCAGCCACTGTGGGGCTAGCCTTCAGA
GCAGATGAAGCCTTTGAGACCCTGCACATCCAGCCCTTCTCCAGCCCACGTGAGCTGCTGGAGGTGATGAAGCCACAGGA
CTGAAGAAGGAGCGCCAATGAACAGGCTCTG

Alignment

ORF - retro_ttru_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQ
          .DVFLMIRRHKTTIF.DAK.SSTV.ELK.IVEGILK.P..EQ.LYKDDQLLDD.KTLGECGFTSQTA.P.
Retrocopy IDVFLMIRRHKTTIFMDAKKSSTVCELKCIVEGILKWPLVEQWLYKDDQLLDDRKTLGECGFTSQTAWPR

Parental  APATVGLAFRADEAFEALRIEPFSSPPELPDVMKPQDSGSSANEQAV
          APATVGLAFRADEAFE.L.I.PFSSP.EL..VMKPQD...SANEQA.
Retrocopy APATVGLAFRADEAFETLHIQPFSSPRELLEVMKPQD*RRSANEQAL

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_1030 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1030 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 11 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019543	3 retrocopies	retro_btau_142, retro_btau_17, retro_btau_29,
Callithrix jacchus	ENSCJAG00000015347	10 retrocopies	retro_cjac_1593, retro_cjac_1606, retro_cjac_2051, retro_cjac_2613, retro_cjac_2987, retro_cjac_3030, retro_cjac_342, retro_cjac_3819, retro_cjac_639, retro_cjac_959,
Felis catus	ENSFCAG00000004711	2 retrocopies	retro_fcat_112, retro_fcat_40,
Gorilla gorilla	ENSGGOG00000015306	1 retrocopy	retro_ggor_976,
Monodelphis domestica	ENSMODG00000016536	4 retrocopies	retro_mdom_1149, retro_mdom_1617, retro_mdom_1964, retro_mdom_23,
Nomascus leucogenys	ENSNLEG00000009471	2 retrocopies	retro_nleu_295, retro_nleu_89,
Oryctolagus cuniculus	ENSOCUG00000010116	2 retrocopies	retro_ocun_202, retro_ocun_930,
Pongo abelii	ENSPPYG00000007013	1 retrocopy	retro_pabe_74,
Pan troglodytes	ENSPTRG00000007663	1 retrocopy	retro_ptro_857,
Rattus norvegicus	ENSRNOG00000004814	6 retrocopies	retro_rnor_1226, retro_rnor_1275, retro_rnor_185, retro_rnor_1948, retro_rnor_35, retro_rnor_352,
Tursiops truncatus	ENSTTRG00000015454	5 retrocopies	retro_ttru_1030 , retro_ttru_109, retro_ttru_1276, retro_ttru_1909, retro_ttru_273,