RetrogeneDB ID: retro_ttru_1679

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_85176:40031..40575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSTTRG00000014186
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_ttru_1679
GTGGGGCATATCTTTGCAAACCTCTTCAAGGGCCTTTCTGGCAAAAAAGAAATGTGCGTTCTCATGGTGGGCCTAGATGC
TGTGGGAAAGACCACTATCCTATACAAACTGAAGCTGGGTGAAATCGTGACCACGATTCCCACTCTAGGCTTCAACGTGG
AAACCGTGGAATACAAGAACATCAGCTTCACTGTGTGGGACATGGGAGGCCAGGACAAGATCTGGCCTCTGTGGTACCAC
TTCTTCCAGAACACACAAGGTCTCGTCTTCATGGTTGACAGCAAGGACAGAGAGCCTGTGAATGAGGCCCGAGAGGAGCT
TATGAGGATGCTGGCAGAAGACGTGCTCAGGGATGCTGTTCTGCTCAGAGTTTGCTAACAAACAGGACCTCCCCAATGCC
ATGAATGCAGCTGAGATCACAGACAAGCTGGGTCTGCACTCTCTGTGCCACAGGAACTGGTACATTCAGGCCACCTGTGC
CACCAGCGGGGACGGGCTCTATGAGGGACTGGACTGGCTGTCCAATCAGCTCCAGAACCAGAAG

Alignment

ORF - retro_ttru_1679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          .G.IFANLFKGL.GKKEM..LMVGLDA.GKTTILYKLKLGEIVTTIPT.GFNVETVEYKNISFTVWD.GG
Retrocopy VGHIFANLFKGLSGKKEMCVLMVGLDAVGKTTILYKLKLGEIVTTIPTLGFNVETVEYKNISFTVWDMGG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLL-VFANKQDLPNAMNAAEI
          QDKI.PLW.H.FQNTQGL.F.VDS.DRE.VNEAREELMRMLAED.LRDAVLL..FANKQDLPNAMNAAEI
Retrocopy QDKIWPLWYHFFQNTQGLVFMVDSKDREPVNEAREELMRMLAEDVLRDAVLL>EFANKQDLPNAMNAAEI

Parental  TDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          TDKLGLHSL.HRNWYIQATCATSGDGLYEGLDWLSNQL.NQK
Retrocopy TDKLGLHSLCHRNWYIQATCATSGDGLYEGLDWLSNQLQNQK

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_1679 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1679 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 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,
Tursiops truncatus	ENSTTRG00000006043	1 retrocopy	retro_ttru_493,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679 , retro_ttru_347,
Tursiops truncatus	ENSTTRG00000015381	1 retrocopy	retro_ttru_284,