RetrogeneDB ID: retro_ttru_1235

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_108102:27565..28022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000003311
• Aliases: None
• Description: None

Sequence

>retro_ttru_1235
ATGGCCGGGCTGCCCTGCACGATTATCAAGGAAACCCAGCGTTTGCTGGCAGAGCCAGTTCCCGGCATTAAAGCAGAACC
AGATGAGAGCAGCGCCCGTTATTTTCATGTGGTCATTGCTGGCCCTCAGGATTCCCCCTTTGAGGGAGGAACTTTTAAAC
TTGAACTATTCCTTCCAGAAGAATACCCAATGGCAGCCCCTAAAGTACGTTTCATGACCAAAATTTATCATCCTAATGTA
GACAAGTTGGGAAGAATATGTTTTAGATATTTTGAAAGATAAGTGGTCCCCAGCACTGCAGATCCGCGCAGTCCTGCTAT
CGATCCAGGCTTTGTTAAGTGCTCCCGACCCAGATGACCCATCAGCAGATGATGTAGCGGAGCAGTGGAAGACCAACGAA
GCCCAAGCCATAGAAACAGTTAGAGCATGGACTAGGCTATATGCCATGAATAATATT

Alignment

ORF - retro_ttru_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGLPRQDIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
          M.GLP...IKETQRLLAEPVPGIKAEPDES.ARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
Retrocopy MAGLPCTIIKETQRLLAEPVPGIKAEPDESSARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR

Parental  FMTKIYHRNVDKLGRIC-LDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKSNEAQAIET
          FMTKIYH.NVDKLGRIC.LDILKDKWSPALQIR.VLLSIQALLSAP.PDDP.A.DVAEQWK.NEAQAIET
Retrocopy FMTKIYHPNVDKLGRIC>LDILKDKWSPALQIRAVLLSIQALLSAPDPDDPSADDVAEQWKTNEAQAIET

Parental  ARAWTRLYAMNNI
          .RAWTRLYAMNNI
Retrocopy VRAWTRLYAMNNI

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_1235 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1235 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 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tupaia belangeri	ENSTBEG00000012497	10 retrocopies	retro_tbel_108, retro_tbel_1208, retro_tbel_1235, retro_tbel_1727, retro_tbel_2393, retro_tbel_2732, retro_tbel_275, retro_tbel_3151, retro_tbel_4655, retro_tbel_849,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,
Tursiops truncatus	ENSTTRG00000003311	3 retrocopies	retro_ttru_1235 , retro_ttru_286, retro_ttru_702,