RetrogeneDB ID: retro_ttru_1022

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100236:26146..26960(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD1
• Ensembl ID: ENSTTRG00000001010
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [Source:HGNC Symbol;Acc:11106]

Sequence

>retro_ttru_1022
GACAAGGACCTGTACGAGCCAGACAACCATCTGGTAGAATGGTACAGAACCGTCACTACCCAGGAGACAGATGACTTCGA
AGTGAAGAGTCCAGAAGATGTGAATGTACGATGTACTGTCCTGCTGATGCTGAGTTACCAGCCTCCTCAGTTTAAATTAG
ACCCTCCTCTGGCTCGGCCGCTAGGCACCCACACCCAGACCCGTCCAGTGACCATTCAAGCACTGTGGCGATATATTAAG
ACGCGTAAGCTCCAGGACCCACCTGAGCGGGAGTTTGTCATCTGTGACAAGTACCTCCAGCAGATCTTTGAGTCTCAACG
TATGAAGTTTTTCAGAGATCCCGCAACGGCTCCATGCCTTGCTTATGCCACCAGAGCCCATCATCGTTAATCATATCATT
AGTGTTGACCCGAATGATCAGGAAAAGACAGCTTGTTATGACATTGATGTGGAAGCAGATGATACCTTGAAGACCCAGAT
GAATTCTTTTCTGTTGTCTACTGCCAGCCAGCAGGAGATTGCTACTCTAGACAGCAAGATCCATGAGACAATAGAAACTA
TCAATCAGCTGAAGACCCAGCGAGAGTTCATGCTGAGCTTTGCCAGAGACCCTCAGGGTTTCATCAATGACTGGCCTCAG
TCCCAGTGCTGGGACCTCAAGACCATGACTGATGTGGTGGGTAACCCAGAGGAAGAGCGCTGAGCTGAGCTCTACTTCCA
GCCTTGGGCACAGGAGGCCATGTGCCAATACTTCTACTCCAAGGTGCAGCAGAGATGACAAGAATTAGAGCAAGCCCTGA
GAATCCGAAATACA

Alignment

ORF - retro_ttru_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.34 %
• Parental protein coverage: 52.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKDLYGPDNHLVEWHRTATTQETDGFQVKRPGDVNVRCTVLLMLDYQPPQFKLDPRLARLLGIHTQTRPV
          DKDLY.PDNHLVEW.RT.TTQETD.F.VK.P.DVNVRCTVLLML.YQPPQFKLDP.LAR.LG.HTQTRPV
Retrocopy DKDLYEPDNHLVEWYRTVTTQETDDFEVKSPEDVNVRCTVLLMLSYQPPQFKLDPPLARPLGTHTQTRPV

Parental  IIQALWQYIKTHKLQDPHEREFVICDKYLQQIFESQRMKF-SEIPQRLHALLMPPEPIIINHVISVDPND
          .IQALW.YIKT.KLQDP.EREFVICDKYLQQIFESQRMKF.SEIPQRLHALLMPPEPII.NH.ISVDPND
Retrocopy TIQALWRYIKTRKLQDPPEREFVICDKYLQQIFESQRMKF>SEIPQRLHALLMPPEPIIVNHIISVDPND

Parental  QKKTACYDIDVEVDDTLKTQMNSFLLSTASQQEIATLDNKIHETIETINQLKTQREFMLSFARDPQGFIN
          Q.KTACYDIDVE.DDTLKTQMNSFLLSTASQQEIATLD.KIHETIETINQLKTQREFMLSFARDPQGFIN
Retrocopy QEKTACYDIDVEADDTLKTQMNSFLLSTASQQEIATLDSKIHETIETINQLKTQREFMLSFARDPQGFIN

Parental  DWLQSQCRDLKTMTDVVGNPEEERRAEFYFQPWAQEAVCRYFYSKVQQRRQELEQALGIRNT
          DW.QSQC.DLKTMTDVVGNPEEER.AE.YFQPWAQEA.C.YFYSKVQQR.QELEQAL.IRNT
Retrocopy DWPQSQCWDLKTMTDVVGNPEEER*AELYFQPWAQEAMCQYFYSKVQQR*QELEQALRIRNT

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_1022 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1022 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037935	1 retrocopy	retro_btau_1829,
Tursiops truncatus	ENSTTRG00000001010	2 retrocopies	retro_ttru_1022 , retro_ttru_1038,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394,