RetrogeneDB ID: retro_ttru_1641

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_82415:5306..6500(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFRD1
• Ensembl ID: ENSTTRG00000010976
• Aliases: None
• Description: interferon-related developmental regulator 1 [Source:HGNC Symbol;Acc:5456]

Sequence

>retro_ttru_1641
TCATCATCAGGTGGCCAGCATCGAAATGTTCAACCTTTTAGTGATGAGGATGCATCGATTGAAACAATGAGCCATTGCAG
TGGTTACAGTGATCCTTCCAGTTTTGCTGAAGATGGACCAGAAGTCCTCGATGAGGAAGGAACTCAAGAAGACTTAGAGT
ATAAGTTGAAGGGATTCATTGACCTGACCCTAGATAAGAGTGCGAAGACAAGGCAGGCAGCTCTTGAAGGTATTAAAAAT
ATACTGGCTTCAAAGATGCTTTATGAATTTATTCTGGAAAGAAGAATGACTTTAACTGATAGCATTGAACGCTGCCTGAA
AAAAGGTAAAGGTGATGAGCAGCGTGCAGCTGCAGCATTAGCATCTGTTCTCTGTATTCAGTTGGGCCCTGGAATTGAAA
GTGAAGAGGTTTTAAAGACTCTTGGACCAATCCTGAAGAAAATAATTTGTGATGGAACAGCTAGTATCCAGGCTAGGCAA
ACTTGTGCAACTTGCTTTGCTGTTTGCTGTTTTATTGCCACAGATGACATTACTGAGCTGTATTCAACTCTGCAGTGTTT
GGAAAATATCTTCACCAAGTCCTATCTCAAAGAGAACGACACTAATGTTGTCTGCAGCACCCCTACTACAGCGCTTCATA
TCAGCTCACTTCTCGTGTGGACATTATTACTGACCATATGCCCAATCAATGAAGTGAAGAAAAAGCTTGAGGTGCATTTC
CATAAACTTCCAAGCCTCCTCTCTTCTGATGATGTAAACATGAGAATAGCTGCTGGTGAATCTCTGGCACTTCTGTTTGA
ATTGGCCAGAGGAATAGAGAGTGACTTTTTTTACGAAGACATGGAGTCTTTGACTCAGATGCTTAGGGCTTTGGCTACAG
ATGGAACTAAGCACCGGGCCAAAGTGGACAAGAGAAAGCAGCGGTCGGTGTTCAGAGACATCCTTAGGGCGGTAGAGGAA
CGGGATTTTCCAACAGAAACTGTTAAATTTGGTCCTGAACGCATGTATATTGATTGCTGGGTCAAAAAACATACATATGA
CACCTTTAAGGAGGTTCTTGGATCAGGGATGCAGTACCACTTGCAGTCAAATGAATTCCTTCGCAATGTTTTTGAACTTG
GACCCCCAGTGATGCTTGATGCTGCAACACTTAAAACAATGAAGATTTCTCGTTTTGAAAGGCATTTATATAAT

Alignment

ORF - retro_ttru_1641 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.74 %
• Parental protein coverage: 93.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATAGGQHRNVQPFSDEDASIETMSHCSGYSDPSSFAEDGPEVLDEEGTQEDLEYKLKGFIDLTLDKSAKT
          ...GGQHRNVQPFSDEDASIETMSHCSGYSDPSSFAEDGPEVLDEEGTQEDLEYKLKGFIDLTLDKSAKT
Retrocopy SSSGGQHRNVQPFSDEDASIETMSHCSGYSDPSSFAEDGPEVLDEEGTQEDLEYKLKGFIDLTLDKSAKT

Parental  RQAALEGIKNILASKMLYEFILERRMTLTDSIERCLKKGKGDEQRAAAALASVLCIQLGPGIESEEVLKT
          RQAALEGIKNILASKMLYEFILERRMTLTDSIERCLKKGKGDEQRAAAALASVLCIQLGPGIESEEVLKT
Retrocopy RQAALEGIKNILASKMLYEFILERRMTLTDSIERCLKKGKGDEQRAAAALASVLCIQLGPGIESEEVLKT

Parental  LGPILKKIICDGTASIQARQTCATCFAVCCFIATDDITELYSTLQCLENIFTKSYLKENDTNVVCSTPTT
          LGPILKKIICDGTASIQARQTCATCFAVCCFIATDDITELYSTLQCLENIFTKSYLKENDTNVVCSTPTT
Retrocopy LGPILKKIICDGTASIQARQTCATCFAVCCFIATDDITELYSTLQCLENIFTKSYLKENDTNVVCSTPTT

Parental  ALHISSLLVWTLLLTICPINEVKKKLEVHFHKLPSLLSSDDVNMRIAAGESLALLFELARGIESDFFYED
          ALHISSLLVWTLLLTICPINEVKKKLEVHFHKLPSLLSSDDVNMRIAAGESLALLFELARGIESDFFYED
Retrocopy ALHISSLLVWTLLLTICPINEVKKKLEVHFHKLPSLLSSDDVNMRIAAGESLALLFELARGIESDFFYED

Parental  MESLTQMLRALATDGTKHRAKVDKRKQRSVFRDILRAVEERDFPTETVKFGPERMYIDCWVKKHTYDTSL
          MESLTQMLRALATDGTKHRAKVDKRKQRSVFRDILRAVEERDFPTETVKFGPERMYIDCWVKKHTYDT..
Retrocopy MESLTQMLRALATDGTKHRAKVDKRKQRSVFRDILRAVEERDFPTETVKFGPERMYIDCWVKKHTYDTFK

Parental  EVLGSGMQYHLQSNEFLRNVFELGPPVMLDAATLKTMKISRFERHLYN
          EVLGSGMQYHLQSNEFLRNVFELGPPVMLDAATLKTMKISRFERHLYN
Retrocopy EVLGSGMQYHLQSNEFLRNVFELGPPVMLDAATLKTMKISRFERHLYN

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_1641 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1641 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004194	1 retrocopy	retro_ogar_695,
Tursiops truncatus	ENSTTRG00000010976	1 retrocopy	retro_ttru_1641 ,