RetrogeneDB ID: retro_ttru_1394

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112252:108929..109655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD2
• Ensembl ID: ENSTTRG00000006988
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Source:HGNC Symbol;Acc:11107]

Sequence

>retro_ttru_1394
GATGATCTTAGGAAACAGAAGAGGAAGTTTTCTTAATTCTTTAAGAGCCTCGTCATGAGCTGGACAAGGAACTGTACGGG
TCTGACAACCACTGCTGGAGTGGCACCGGATGCCCACCACCAGGAGACAGATGGCTTTCAGGTGAAACCGCCTGGAAACC
TCAACGTCAAGTGCACCTGCCTGCTCCTGCTGGCTCATCAGCCTCCCCAGTACAAGTCGGACCCCCGACTGGGGAGGCCG
CTGGGGGTGCACACACACACGAGGGCTGCCGTCACGCAGGCCCTGCGGCTCTACATCAAACACAACCAGCTGCAGGACGG
CCACGAGCGGGAGTACGTCAGCTGCAACCGGTACTTCTGCCAGATCTTCACCTGTGGCCGACTGCGTTTCTCTGAGATTC
CCATGAAGCTAGCCAGGTTGCCGCAGCCTCCAGACCCCATTGTCGTCAACCATGTAATTAGCTTGGACCCTAACAACCAG
AAGAAGACAGGCTGTTATGACATTGATGTGGAGGTGGATGACCCACTCAAGGCCCAGATGAGCAATTTTCTGGCCTCTAC
CACCAATCAGCAGGAGATTGCCTCCCTTGATGTCAAAATCCATGAGACCATTGAGTCCATCAACCAGCTGAAGACCCAGA
GGGATCTCATGCTCAGTTTTAGCACTGACCCCCAGGACTTCATCCAGGAATGGCTCCGTTCCCAGCGCTGGGACCTCAAT
CTGATG

Alignment

ORF - retro_ttru_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 51.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDPSKQKRKFSSFFKSLVI-ELDKELYGPDNH-LVEWHRMPTT-QETDGFQVKRPGDLNVKCTLLLMLDH
          DD..KQKRKFS.FFKSLV..ELDKELYG.DNH.L.EWHRMPTT.QETDGFQVK.PG.LNVKCT.LL.L.H
Retrocopy DDLRKQKRKFS*FFKSLVM<ELDKELYGSDNH<LLEWHRMPTT<QETDGFQVKPPGNLNVKCTCLLLLAH

Parental  QPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEREYINCNRYFRQIFSCGRLRFSEIPMK
          QPPQYK.DPRL.R.LGVHT.TRAA..QAL.LYIKHNQLQDGHEREY..CNRYF.QIF.CGRLRFSEIPMK
Retrocopy QPPQYKSDPRLGRPLGVHTHTRAAVTQALRLYIKHNQLQDGHEREYVSCNRYFCQIFTCGRLRFSEIPMK

Parental  LAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDVKIHETIES
          LA.L.Q.PDPIV.NHVIS.DPN.QKKT.CYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDVKIHETIES
Retrocopy LARLPQPPDPIVVNHVISLDPNNQKKTGCYDIDVEVDDPLKAQMSNFLASTTNQQEIASLDVKIHETIES

Parental  INQLKTQRDFMLSFSTDPQDFIQEWLRSQRRDLKII
          INQLKTQRD.MLSFSTDPQDFIQEWLRSQR.DL...
Retrocopy INQLKTQRDLMLSFSTDPQDFIQEWLRSQRWDLNLM

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_1394 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1394 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012708	1 retrocopy	retro_cfam_256,
Callithrix jacchus	ENSCJAG00000019528	1 retrocopy	retro_cjac_2323,
Mustela putorius furo	ENSMPUG00000014835	1 retrocopy	retro_mputfur_89,
Sarcophilus harrisii	ENSSHAG00000013118	1 retrocopy	retro_shar_464,
Tursiops truncatus	ENSTTRG00000001010	2 retrocopies	retro_ttru_1022, retro_ttru_1038,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394 ,