RetrogeneDB ID: retro_ttru_1423

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112896:100758..101598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMBS
• Ensembl ID: ENSTTRG00000002806
• Aliases: None
• Description: hydroxymethylbilane synthase [Source:HGNC Symbol;Acc:4982]

Sequence

>retro_ttru_1423
ACCAAGGAGCTGGAACATGCACTGGAGAGGAATGAAGTGGACCTGGTTGTTCACTCCCTGAAGGACCTGCCCATGGTGCT
TCCTCCTGGCTTCACCATTGGAGCCATTTGCAAGCAGGAGAGCCCCTCTGATGCTGTTGTCTTTCACCCAAATTTTGTTG
GGCAGACCCTAGAAACCTTGCCAGGGAAGAGCGTGGTGGGAACTAGCTCCCTGCGGAGAGCGGCCCAGCTGCAGAGAAAG
TTCCCACATCTGGAGTTCAAGAGTATTCGGGGAAACCTCAACACACGGCTTTGGAAGTTGGATGAGCTGCAGGAGTTCAG
TGCCATCATCCTGGCTGTAGCTGGCCTGCAGTGCATGGGCTGGCAGAACCAGGTGGGACAGATCCTGCACCCTGAGGAGT
GCAGGTTGGGGGCTCTGGGAGTGGAAGTTCAAGCCAAGGACCAGGACATCTTGGATCTGGTGGGTGTGTTGCATGATCCT
GAGACTCTGCTTCACTGCACTGCTGAACGGGCCTTCCTGAGGTACCTGGAAGGAGGCTGCAGTGTGCCAGTGGCAGAGCA
TACAGCTATGAAGGATGGGCAACTCTACCTGACTGGAGGAGTCTGGAGTCTGAATGGCACAGATAACATGCAAGAGACCA
TGCAGGCCACCATCCGTGTCCCTGCCCAGCATGAAGATGGCCCTGAGGATGATCCACAGCTGGTGGGCATCACTGCCCGG
AACATTCCACGACAAGCCCAGCTGGCTGCTGAGAGCCTGGGCATCAGCCTGGCCACCTTGCTGCCGAACAAAGGAGCCAA
GAACATCTTGGATGTTGCACGGCAGCTCAATGATGCCCAC

Alignment

ORF - retro_ttru_1423 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 86.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKELEHALERNEVDLVVHSLKDLPTVLPPGFTIGAICKRESPYDAVVFHPKFVGKTLETLPEKSLI---T
          TKELEHALERNEVDLVVHSLKDLP.VLPPGFTIGAICK.ESP.DAVVFHP.FVG.TLETLP.KS......
Retrocopy TKELEHALERNEVDLVVHSLKDLPMVLPPGFTIGAICKQESPSDAVVFHPNFVGQTLETLPGKSVVGTSS

Parental  ISLAAQLQRKFPHLKFKS-RGNLNTRLRKLDELQEFSAILLAAPGLQRMGWQN---RILHPEECMYAVGQ
          ...AAQLQRKFPHL.FKS.RGNLNTRL.KLDELQEFSAI.LA..GLQ.MGWQN....ILHPEEC....G.
Retrocopy LRRAAQLQRKFPHLEFKSIRGNLNTRLWKLDELQEFSAIILAVAGLQCMGWQNQVGQILHPEEC--RLGA

Parental  GALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLNG
          ....V.....D..ILDLVGVLHDPETLL.C.AERAFLR.LEGGCSVPVA.HTAMKDGQLYLTGGVWSLNG
Retrocopy LGVEVQAKDQD--ILDLVGVLHDPETLLHCTAERAFLRYLEGGCSVPVAEHTAMKDGQLYLTGGVWSLNG

Parental  ADSMQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRRAQLAAESLGISLATLLLNKGAKNILDVARQL
          .D.MQETMQATI.VPAQHEDGPEDDPQLVGITARNIPR.AQLAAESLGISLATLL.NKGAKNILDVARQL
Retrocopy TDNMQETMQATIRVPAQHEDGPEDDPQLVGITARNIPRQAQLAAESLGISLATLLPNKGAKNILDVARQL

Parental  NDAH
          NDAH
Retrocopy NDAH

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_1423 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1423 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
Callithrix jacchus	ENSCJAG00000013900	1 retrocopy	retro_cjac_1019,
Tursiops truncatus	ENSTTRG00000002806	1 retrocopy	retro_ttru_1423 ,