RetrogeneDB ID: retro_ttru_1613

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_63162:163..859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSTTRG00000014870
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_ttru_1613
ATGAATTCAGGAAGACCCGAGACCATGGAGAACTTGCCTGCTCTCTACACTATTTTCCAAGGAGAGGTTGCTATGGTGAC
AGACTGTGGAGGCAAGTCAAAATCCCAGGCTGTCGGAAGCAAGGTCTGGTCCATCGAACTCACATGTCATCCTGTCGCGT
GGATAAGCCCTCTGAGATAGTAGATGTCGGAGAGAAGGTGTGGGTGAAGCTTATCGGACGAGAGATGAAAAGGGAAAGGA
TAAAAGTATCCCTCTCCGTGAAAGCTGTCAACCAAGGGACTGGGAAGGACCTTGACGCCAACAACGTTATCATTGAGCAA
TAAGAGAGGCAGAGGCAGTCCTTCCAGGATTACACTGGGCAGAAGATCACCCTCGAGGCTGTCCTGAACACTACCTGCAA
GGAGTGTGGCTGTAAAGGCCACTTCGCAAAGCATTGTTTCATGCAACCAGGTGGGAGCAAGTACTCTCTGATACCTAATG
AGAGAGAGGAGAAGGAAGAGGCAAAATCAGCAGAGTTTGAAAAGCCTGACCCCACGAGAAATTCTTCTAGAAAAAGAAAG
AAGGAAAAGGAGAAAAAGAAACAGAGAGACAGGAAGTCATCTGACTCTGACAGCTCGGACTCTGAGAGTGACACACAAGA
GGGCAAGGCACACGTCAAAAGACAGCAAGGCAGCAAAGAAGAAAAAGAAGAAGCAG

Alignment

ORF - retro_ttru_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 96.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSGRPETMENLPALYTIFQGEVAMVTDYGAF-IKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWV
          MNSGRPETMENLPALYTIFQGEVAMVTD.G....KIPGCRKQGLVHRTHMSSCRVDKPSEIVDVG.KVWV
Retrocopy MNSGRPETMENLPALYTIFQGEVAMVTDCGGK<VKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGEKVWV

Parental  KLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCK
          KLIGREMK..RIKVSLS.K.VNQGTGKDLD.NNVIIEQ.ER.R.SFQDYTGQKITLEAVLNTTCK.CGCK
Retrocopy KLIGREMKRERIKVSLSVKAVNQGTGKDLDANNVIIEQ*ERQRQSFQDYTGQKITLEAVLNTTCKECGCK

Parental  GHFAKDCFMQPGGTKYSLIPDEEEEKEEAKAAEFEKPDPTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSE
          GHFAK.CFMQPGG.KYSLIP.E.EEKEEAK.AEFEKPDPTRNSS.................SDSDSSDSE
Retrocopy GHFAKHCFMQPGGSKYSLIPNEREEKEEAKSAEFEKPDPTRNSSXXXXXXXXXXXXXXXXXSDSDSSDSE

Parental  SDTGKRARHTSK-DSKAAKKKKKK
          SDT.....H.......A.KKKKK.
Retrocopy SDTQEGKAHVKR>SKAAKKKKKKQ

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_1613 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1613 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613 ,