RetrogeneDB ID: retro_ttru_1237

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108235:225782..226339(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSTTRG00000005833
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_ttru_1237
CTCGCCGGCCCCGCCATGGTATTTCTCGATTTTTGGATGATGATGTGCAGCGGATGAACAAGCGGCAGCTCTATTATCAA
GTCCTAAATTTTGGAAAGACTGTCTCCTCGGCACCAGTGCCCTGGAAGGGGTTAACGGTTATAACTGGAAGGGAAAGTCC
CGTTGCCGTGGTGCTCGGCGGCAGCACGGAACGTGCATTTCATAGAGGAGATTTTCTCTTGCTAGCAAGTCGAGTTGAAG
ATCATCCCGTAGGAGTGGAAGAAATTGTTGTTTTTAGGATAGAAGGAAGAGAGGTTCCTATAGTTCACCGAGTCTTGAAG
ATTCATGAAAAGCAAAATGGACCTGTGAAGTTTCTGACCAAAGGAGGTAACAGTGTGGTTGATGCCCGAGGCCTGTATAA
ACAAGGACGACATTGGCTAGAGAAGAACGATGTTGTGAGGACAGCGAGGGGATTTGTTCCTTACACTGGGGTTGGGACCA
TCCTCATGAGTGACTATCCTAAGTTTCAGTGTGCAGTACTCTTCTTGCTGGGTTTATTTGTGCTGGTCCATCGTGAG

Alignment

ORF - retro_ttru_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.94 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAGPAMLSLD-FLDD-VRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHR
          LAGPAM..LD.FLDD.V.RMNKRQLYYQVLNFG..VSSA...WKGL.VITG.ESP..VVL.GS.E.AFHR
Retrocopy LAGPAMVFLD<FLDDDVQRMNKRQLYYQVLNFGKTVSSAPVPWKGLTVITGRESPVAVVLGGSTERAFHR

Parental  GDLLFLTNRVED-PIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHW
          GD.L.L..RVED.P..V.EIVVFRIEGRE.PIVHRVLKIHEKQNG..KFLTKG.N..VD.RGLYKQG.HW
Retrocopy GDFLLLASRVEDHPVGVEEIVVFRIEGREVPIVHRVLKIHEKQNGPVKFLTKGGNSVVDARGLYKQGRHW

Parental  LEKKDVVGRARGFVRYIGIVTILMNDYRK-KYAVLFLLGLFVLVHRE
          LEK.DVV..ARGFV.Y.G..TILM.DY.K...AVLFLLGLFVLVHRE
Retrocopy LEKNDVVRTARGFVPYTGVGTILMSDYPKFQCAVLFLLGLFVLVHRE

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_1237 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1237 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237 ,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,