RetrogeneDB ID: retro_ttru_1083

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102326:64438..64828(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA1
• Ensembl ID: ENSTTRG00000015539
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 1 [Source:HGNC Symbol;Acc:28109]

Sequence

>retro_ttru_1083
AAAATAGGAGATGAGATCATTGCAGTAAATGAACTTCTAAATAAATTGGAATTGGAAATTCAGTATCAAGAACAAACCAA
CAATTCACTCAAGGAACTCTTTGAACCTCTTGGAGAAGATTGTAAAGATGGAACATCTCAAAGAAAACATTCCTTCCCAT
TTGCCTCAAGTAACCCAGAACTTTGTAATGGATCAGATCTTGACCCTGAACAACCAGTCAAAGATGAGGAACCTGCACCC
ACAAAGAAGCCCCCCAAAGAGCAAAGAAATATTAAAGAAATGTCATTTATAACTTCTGATGAGTTTAATGGCATTCTTGT
GTACATGAAATCCCACCTAACCTATTGTCAAATTAACGACATAACCTAACCTATTGTCAAATTAATGATG

Alignment

ORF - retro_ttru_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KIGDEIIVVNELLNKLELEIQYQEQTNSSLKELFE-CLEEDYKDVEHLKENIPPHLPQVTVTQNIV-NGS
          KIGDEII.VNELLNKLELEIQYQEQTN.SLKELFE..LE...K..EHLKENIP.HLPQVT..QN.V.NGS
Retrocopy KIGDEIIAVNELLNKLELEIQYQEQTNNSLKELFE>LLEKIVK-MEHLKENIPSHLPQVT--QNFV<NGS

Parental  DLDPEEPVKVEEAAPTKKPSKEQKHVKEMPFVTSDEFSGIPAYMKSRLTYCQINDVIKEINKAVV
          DLDPE.PVK.EE.APTKKP.KEQ...KEM.F.TSDEF.GI..YMKS.LTYCQIND....I.K...
Retrocopy DLDPEQPVKDEEPAPTKKPPKEQRNIKEMSFITSDEFNGILVYMKSHLTYCQINDIT*PIVKLMM

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_1083 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1083 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008555	2 retrocopies	retro_cjac_1103, retro_cjac_875,
Dasypus novemcinctus	ENSDNOG00000000190	1 retrocopy	retro_dnov_1081,
Loxodonta africana	ENSLAFG00000005238	1 retrocopy	retro_lafr_849,
Myotis lucifugus	ENSMLUG00000013388	1 retrocopy	retro_mluc_2127,
Sus scrofa	ENSSSCG00000004518	1 retrocopy	retro_sscr_360,
Tursiops truncatus	ENSTTRG00000015539	1 retrocopy	retro_ttru_1083 ,