RetrogeneDB ID: retro_ttru_400

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_214:446406..447186(-)
• Located in intron of: ENSTTRG00000015684

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSTTRG00000002384
• Aliases: None
• Description: eukaryotic translation initiation factor 5 [Source:HGNC Symbol;Acc:3299]

Sequence

>retro_ttru_400
ATGTCTGTCAACGTCAACCGCAGCGTGTCAGACCAGTTCTATCGCTACGAGATGCCTCGTCTGATTGCCAAAGTTGAGGG
CAAAGGAAATGGAATCAAGACAGTTATAGTCAACATGGTTGACATAGCCGAAGCGCTTAATCAGCGTCCAACGTATCCCA
CCGAATATTTAGGTTGCGAACTGGGAGCACAGACCCAGTTTGATGTTAAGAATGACCGTTACATTGCCAGTGGATCTCAT
GAGGCGAATAAGCTGCAAGGCATGTTGGATGGATTCATTAAAAAATCTGTTCTCTGTCCTGAGTGTGAGAATTCCGAAAT
GGATGTGCATGTCAATCCAAAGAAGCAAACAATAGGTAATTCTTGTAAAGCCTGGGGCTATCGAGGCATGCTTGACACAC
ATCATAAACTCTGCATGTTCATTCTCAAAATGCCACCTGAGAATAGTGACGATGGTTCAGGAAAGAAAGAAAAGGAAAAG
AAAACTAGAAAGGGCAAAGACAAGGGAAATGGCTCCGTGTCCAGCAGTGAGACACCACCTCCACCACCACCCAATGAAAT
CTGTCCTCCTCCACATGCTGTGGAAGAAGAGGAGGATGATGACTGGGGGGAGGATACAACAGAGGAAGCTCAAAGGGGAA
GAATGGATGAAATCAGTGACCACGCAAAAGTTTTAACCCTCAGTGATGATTTGGAATGGACTGTTGAAGAGCGTGTCAAT
ATCCTGTTTGATTTTCTTAAGAAAAAGAAAGAAGACGGTAGTATTGACCCATCTGACAAA

Alignment

ORF - retro_ttru_400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 73.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVNVNRSVSDQFYRYKMPRLIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYFGCELGAQTQFDVK
          MSVNVNRSVSDQFYRY.MPRLIAKVEGKGNGIKTVIVNMVD.A.ALN..PTYPT.Y.GCELGAQTQFDVK
Retrocopy MSVNVNRSVSDQFYRYEMPRLIAKVEGKGNGIKTVIVNMVDIAEALNQRPTYPTEYLGCELGAQTQFDVK

Parental  NDRYIVNGSHEANKLQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTF
          NDRYI..GSHEANKLQ.MLDGFIKK.VLCPECEN.E.D.HVNPKKQTIGNSCKA.GYRGMLDTHHKLC.F
Retrocopy NDRYIASGSHEANKLQGMLDGFIKKSVLCPECENSEMDVHVNPKKQTIGNSCKAWGYRGMLDTHHKLCMF

Parental  ILKNPPENSDSGTGKKEKEKKNRKGKDKENGSMSSSETPPPPPPPSEISPPHAVEEEEDDDWGEDTTEEA
          ILK.PPENSD.G..................GS.SSSETPPPPPP.....PPHAVEEEEDDDWGEDTTEEA
Retrocopy ILKMPPENSDDGSXXXXXXXXXXXXXXXXXGSVSSSETPPPPPPNEICPPPHAVEEEEDDDWGEDTTEEA

Parental  QRRRMDEISDHAKVLTLSDDLERTVEERVNILFDFVKKKKEEGVIDSSDK
          QR.RMDEISDHAKVLTLSDDLE.TVEERVNILFDF.KKKKE.G.ID.SDK
Retrocopy QRGRMDEISDHAKVLTLSDDLEWTVEERVNILFDFLKKKKEDGSIDPSDK

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_400 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_400 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Echinops telfairi	ENSETEG00000015220	2 retrocopies	retro_etel_1843, retro_etel_991,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,
Tursiops truncatus	ENSTTRG00000002384	1 retrocopy	retro_ttru_400 ,