RetrogeneDB ID: retro_ttru_1900

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97950:15936..16895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSTTRG00000010235
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_ttru_1900
GAGCGTGATCCCAGGACAATACCTCCACCACCACCTCCTCCCAGAAAGGAGACCAAGCCAGAGCCAATGGAAAAAGATCT
TCAGGAGAGTAAGAAGCAGGCACTGAAAGGAAAAGAATTGGGGAATGATGCTTGTAAGAAGAAAGATTCTGACGCAACCT
TGAAGCTCTATGACAGAGCCACAGGCCTGGACCCCACCAACATTACTTTTGTGACCAACCAAGCAGCCGTGTACATTGAA
AAGGGCAACTACAGTGAATTCCGGGAGCTTTTTGAGAAGGCCATTGAAGTTGGCCCAGAAGACTACCGACAGACTACCAG
AGCTTATGCTCAAATTGGCAACGCCTATTTCAAAGAAAAGTACAAGGGTGCCATACATTTCTACAACAAGTCTCTGGCAG
AGCACTGAACCCCAGATGTGCTCAAGAAATGCCAACAGGAAGAGAAAATCCTGCAGGAGCAGGAGTGACTGGCCTACATA
AACCCTGAGTGGGCTTTAGAGGAGAAGAACAAAGGCAATGCATGTTTTCAGAAAAGGAACTATCCCCAGGCCAGGAAGCA
TTAAATGGAAGCCATCAAACAGAACTCAAAAGATGCTAAATGGTACAGCAATCAAGCTTCCTGCTATAGCAAACTCTTGG
AGTTTCAGATGGCACTCAAGGACTGGGAGGAATGTATCCCGCTAGAGCCAACGTTCATCAAGGGCTATACATGGAAAGCA
GCTGCCCTAGAAGTGACGAAAGACTACCCAAAGGCCACAAATGTCTACCAGAAGGCATCAGACCTGGACGCCAACTGTAA
AGGAAGCAGCAGATGGTTACCAATGCTACCTCATGGCCCAGTACAACCAACACGACAGCCTGAAGATGTGAAGTGATGGG
CCGTGGCTGCCTTGAGGTGCAGCAGATAATGAATGACCCGGCCATGCAGCTTATCCTGGAACAGGTGCAGCAGTACCCC

Alignment

ORF - retro_ttru_1900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.48 %
• Parental protein coverage: 55.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEEEVVTPPPPPPPRKETKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDPTNMTY
          E......PPPPPPPRKETKPEPME.DL.E.KKQALK.KELGN.A.KKKD.D..LK.YDRA..LDPTN.T.
Retrocopy ERDPRTIPPPPPPPRKETKPEPMEKDLQESKKQALKGKELGNDACKKKDSDATLKLYDRATGLDPTNITF

Parental  ITNQAAVYFEKGDYGKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHR
          .TNQAAVY.EKG.Y...REL.EKAIEVG....EDYRQ...AYA.IGN.YFKE.KYK.AIHFYNKSLAEH.
Retrocopy VTNQAAVYIEKGNYSEFRELFEKAIEVGP---EDYRQTTRAYAQIGNAYFKE-KYKGAIHFYNKSLAEH*

Parental  TPDVLKKCQQAEKILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRA
          TPDVLKKCQQ.EKIL.EQE.LAYINP..ALEEKNKGN.CFQK..YPQA.KH..EAIK.N.KDAK.YSN.A
Retrocopy TPDVLKKCQQEEKILQEQE*LAYINPEWALEEKNKGNACFQKRNYPQARKH*MEAIKQNSKDAKWYSNQA

Parental  ACYTKLLEFQLALKXXXXXXXXEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSNC-KEAADGYQR
          .CY.KLLEFQ.ALK........EPTFIKGYT.KAAALE..KDY.KA..VYQKA.DLD.NC.KEAADGYQ.
Retrocopy SCYSKLLEFQMALKDWEECIPLEPTFIKGYTWKAAALEVTKDYPKATNVYQKASDLDANC>KEAADGYQC

Parental  CMMAQYNRHDS-PEDVKRRAMAD-PEVQQIMSDPAMRLILEQMQKDP
          ..MAQYN.HDS.PEDVK..A.A...EVQQIM.DPAM.LILEQ.Q..P
Retrocopy YLMAQYNQHDS<PEDVK*WAVAA<LEVQQIMNDPAMQLILEQVQQYP

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_1900 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1900 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900 ,