RetrogeneDB ID: retro_ttru_535

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2618:550667..551687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSTTRG00000005983
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_ttru_535
CAGGATCGCCACGACGCGAGCAGCAATGGGAACCCGCGCCTGCTTCACCTCTCCTCCGCCGGGCAGCATCTCTACAGCCC
CGCGCCGCCCCTCTCCCATGCTGGAGTCGCCGAATACCAGCCACCACCCTACTTTCCGCCTCCCTACCAGCAGCTGGCTT
ACTCGCAGGCAGCCGACCCCTACTCGCATCTGGGAGAAGCGTACGCCGCCGCCATCAACCCCCTGCACCAGCCGGCGCCC
ACCGGCAGCCAGCAGCAGGCCTGGCCGGGCCGCCAGAGCCAGGAGGGGGCTGGGCTGCCCTCGCACCACGCGCGCCCGGC
CGGCTTGTTGCCCCACCTCTCCGGGCTGGACGGCGGCGCCATGAGCGCCCGCAGGGACGCCTACCGCCGCTCGGACCTGC
TGTTGCCCCACTCGCACGCTCTGGACGCCGCGGGCCTGGCCGAGAACCTGGGGCTCCACGACATGGCGCACCAGATGGAG
GAGGTGCAGAATGTCGACGACCAGCACCTACTTCTGCATGATCAGACGGTCATTCGCAAAGGTCCTATTTCAATGACGAA
GAACCCCTTGAGTCTCCCTTGTCAGAAGGAGCTGGTGGAGGCTGTGATGAATCCCAGCGAGGTCTTCTGCTCGGTCCCTG
GAAGATTGTCCCTCCTCAGCTCTACATCTAAATACAAAGTGACAGTTGCCGAAGTCCAGAGGCGACTGTCCCCGCCTGAG
TGCTTATATGCTTCATTACTGGGAGGTGTTCTCAGAAGAGCCAAATCTAAAAATGGTGGCCGATCCTTGCGGGAGAAGTT
GGACAAGATTGGGTTGAATCTTCCAGCGGGGAGACGGAAAGCTGCCCACGTCACCCTCCTGACATCTTTAGTAGAAAGTG
AGGCTGTTCATTTGGCTCGGGACTTTGCCTATGTCTGTGAAGCAGAATTTCCTAGTAAATCCGTGGCCGAGTATTTAACC
AGACCTCATCTCGGAGGACGCAGTGAGATGGCAACTAGGAAGAATATGCTGCTGGCTGCA

Alignment

ORF - retro_ttru_535 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.24 %
• Parental protein coverage: 75.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDRHDASSNGNPRLPHLSSAGQHLYSPAPPLSHAGVAEYQPPPYFPPPYQQLAYSQAADPYSHLGEAYAA
          .DRHDASSNGNPRL.HLSSAGQHLYSPAPPLSHAGVAEYQPPPYFPPPYQQLAYSQAADPYSHLGEAYAA
Retrocopy QDRHDASSNGNPRLLHLSSAGQHLYSPAPPLSHAGVAEYQPPPYFPPPYQQLAYSQAADPYSHLGEAYAA

Parental  AINPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHARPAGLLPHLSGLDGGAVSARRDAYRRSDLLLPHSHA
          AINPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHARPAGLLPHLSGLDGGA.SARRDAYRRSDLLLPHSHA
Retrocopy AINPLHQPAPTGSQQQAWPGRQSQEGAGLPSHHARPAGLLPHLSGLDGGAMSARRDAYRRSDLLLPHSHA

Parental  LDAAGLAENLGLHDMAHQMEEVQNVDDQHLLLHDQTVIRKGPISMTKNPLSLPCQKELVEAVMNPSEVFC
          LDAAGLAENLGLHDMAHQMEEVQNVDDQHLLLHDQTVIRKGPISMTKNPLSLPCQKELVEAVMNPSEVFC
Retrocopy LDAAGLAENLGLHDMAHQMEEVQNVDDQHLLLHDQTVIRKGPISMTKNPLSLPCQKELVEAVMNPSEVFC

Parental  SVPGRLSLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRSLREKLDKIGLNLPAGRRK
          SVPGRLSLLSSTSKYKVTVAEVQRRLSPPECL.ASLLGGVLRRAKSKNGGRSLREKLDKIGLNLPAGRRK
Retrocopy SVPGRLSLLSSTSKYKVTVAEVQRRLSPPECLYASLLGGVLRRAKSKNGGRSLREKLDKIGLNLPAGRRK

Parental  AAHVTLLTSLVEGEAVHLARDFAYVCEAEFPSKSVAEYLTRPHLGGRNEMATRKNMLLAA
          AAHVTLLTSLVE.EAVHLARDFAYVCEAEFPSKSVAEYLTRPHLGGR.EMATRKNMLLAA
Retrocopy AAHVTLLTSLVESEAVHLARDFAYVCEAEFPSKSVAEYLTRPHLGGRSEMATRKNMLLAA

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_535 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_535 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535 ,