RetrogeneDB ID: retro_ttru_564

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2694:153652..154469(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSL1
• Ensembl ID: ENSTTRG00000016584
• Aliases: None
• Description: NSL1, MIS12 kinetochore complex component [Source:HGNC Symbol;Acc:24548]

Sequence

>retro_ttru_564
CTCTCCCCTCTGTGGGACATGGAGAGAGTAGCTGCGATAGATGACAGGGCCTCGGTCCCTGCCACCTCCTGAAAAGACTT
GCAAGTGCGCTGCACCTCAAAGCGGGCAGTGATAGAAATGCTAGAACTGGTGGCAGCTCTGCGCAAAACCTCGGGGACGC
GCTGCCAGAGGAGATTCGGGAGCCCCTGCTGCAAGATGCGCAGTGGACTTCTGAATCAGCTGTGCAAGAGAATGTCAACA
TTCATGGGCAAGCATGGCAGGAAGCTTCAGACAATTGCTTATGGATTCTGATATCAAAGTCCTTGAAAACCAGTTTAATG
AAATCACAGTCCATGTAGCCACAAAACAGTAAGCAGTATCCCAGAAAGATCCTTCAATGTGTCATCAAAATCATAAAAGC
AAAACAAGAAATTCTGAAGCAGTACTAACCTGTTGTACATCCATTGGACCTAAAATATGACCCTGATCCAGCCCCTCGTA
TGGAAAACTTGAACTGCAGAGAAGAAACAATAGCTAAGGAGATGAGTGAAGCTACGAAGTCCTTGCCTGCATTAATTGAA
CAAGGAGATGGATTTTTCCCAAGTTTTAAAGATGCAGCCTATTATCCGGCTCCAGAAAGTCCACCAAGAAGTCTTCTTCG
GGTTGTTATAGGAAACCAGATGTTAAACCTGAGAGCTTTATAGCACAAGTAAAAACCACACCAGTGGAGACTTCTGCTAG
GAAAACCACTGACTTGGTACTGAGAAGGAAGGGAACTAAAGACTGCCGCCAGAGAAAATGGTATCCGTTGAGGCCAGAGA
GAATCAGTCTTGATACA

Alignment

ORF - retro_ttru_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LSAPRDVERVAGTDDGAPVLATSRKDFRVRCTSKRAVTEMLELC-GRFVQKLGDALPEEIREPVLRDAQW
          LS...D.ERVA..DD.A.V.ATS.KD..VRCTSKRAV.EMLEL..G...Q.LGDALPEEIREP.L.DAQW
Retrocopy LSPLWDMERVAAIDDRASVPATS*KDLQVRCTSKRAVIEMLELV<GSSAQNLGDALPEEIREPLLQDAQW

Parental  T-ESAVQ--VSINGQAWQEASDN-YFMDSDIKVLEDQFDEIIVDIATKR-KQYPRKILECVIKIIKAKQE
          T.ESAVQ..V.I.GQAWQEASDN...MDSDIKVLE.QF.EI.V..ATK..KQYPRKIL.CVIKIIKAKQE
Retrocopy TSESAVQENVNIHGQAWQEASDN<LLMDSDIKVLENQFNEITVHVATKQ>KQYPRKILQCVIKIIKAKQE

Parental  ILKQYHPVVHSLDLKHDPDPAPRMENLKCRGEKIAKEISEAMKSLPALIEQGDGF-SQVLKMQPVIQLQR
          ILKQY.PVVH.LDLK.DPDPAPRMENL.CR.E.IAKE.SEA.KSLPALIEQGDGF.SQVLKMQP.I.LQ.
Retrocopy ILKQY*PVVHPLDLKYDPDPAPRMENLNCREETIAKEMSEATKSLPALIEQGDGF>SQVLKMQPIIRLQK

Parental  VHQEVF-SGCCRKPDVKPESFIAQIETTPAESSARKDTDLVLRRKRTKDCPQRKWYPLRPKRISLDT
          VHQEVF.SGC.RKPDVKPESFIAQ..TTP.E.SARK.TDLVLRRK.TKDC.QRKWYPLRP.RISLDT
Retrocopy VHQEVF>SGCYRKPDVKPESFIAQVKTTPVETSARKTTDLVLRRKGTKDCRQRKWYPLRPERISLDT

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_564 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_564 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001862	1 retrocopy	retro_chof_464,
Rattus norvegicus	ENSRNOG00000042286	1 retrocopy	retro_rnor_2027,
Tarsius syrichta	ENSTSYG00000003900	1 retrocopy	retro_tsyr_202,
Tursiops truncatus	ENSTTRG00000016584	1 retrocopy	retro_ttru_564 ,