RetrogeneDB ID: retro_ttru_1365

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111405:44469..45064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000013618
• Aliases: None
• Description: None

Sequence

>retro_ttru_1365
GACGAAGTCATACGGAAGCGTCTCCTCATAGATGGAGATGGTGCTGGAGATGATCGGAGAATTAATCTGCAGGTGAAAAG
TTTCATTAAATGGTACAGCTCTGGATCCCAGGAAGAGGGATACAGCCAGTACCAACGTATGCTGAGCACACTGTCCCAAT
GTGAATTTTCAATGGGCAAAACTTTGCTGGTATATGATATGAATCTCAGAGAAATGGAAGATTTTGAAAAAATTTACAAA
GAACTAGAATGTAGCATTGCTGGAGCACATGAAAAAAATGCTGAGTGCAAAAAGCAAATTATTCAAGCAAAATGAATACG
AAAAAATCGCCAAGAATATGATGCATTGGCAAAAGTGATCTAGCGTCATCCAGACAGGCATGAGACATTAAAGGAACTAG
AGGCTCTGCGTAAAGAATTAGAGCATCTTTCACATATTAAAGAAAGTGTTGAAGATAAGCTAGAATTGAGAAGGAAACAG
TTTCACGTTCTTCTTAGTACCATCCATGAACTTCAGCAAACACTGGAAAATGATGAAAAGCTCTCAGAGGTAGAAGAAGC
TCAAGAAAACAAGCATGGAAACTGATCCTAAACCA

Alignment

ORF - retro_ttru_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLR
          DEVIRKRLLIDGDGAGDDRRINL.VKSFIKW..SGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLR
Retrocopy DEVIRKRLLIDGDGAGDDRRINLQVKSFIKWYSSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLR

Parental  EMENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQRHPDRHETLKELEALGKEL
          EME..EKIYKE.ECSIAGAH...................RQEYDALAKVI.RHPDRHETLKELEAL.KEL
Retrocopy EMEDFEKIYKELECSIAGAHXXXXXXXXXXXXXXXXXXXRQEYDALAKVI*RHPDRHETLKELEALRKEL

Parental  EHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEEAQE-TSMETDPKP
          EHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEEAQE.TSMETDPKP
Retrocopy EHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEEAQE>TSMETDPKP

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_1365 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1365 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 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097,
Echinops telfairi	ENSETEG00000015076	3 retrocopies	retro_etel_1093, retro_etel_1858, retro_etel_85,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Macropus eugenii	ENSMEUG00000006342	4 retrocopies	retro_meug_1481, retro_meug_1524, retro_meug_1599, retro_meug_1861,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Monodelphis domestica	ENSMODG00000003009	1 retrocopy	retro_mdom_315,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031, retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sarcophilus harrisii	ENSSHAG00000011615	1 retrocopy	retro_shar_240,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365 , retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,