RetrogeneDB ID: retro_ttru_1315

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110308:111602..112644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC5
• Ensembl ID: ENSTTRG00000000542
• Aliases: None
• Description: THO complex 5 [Source:HGNC Symbol;Acc:19074]

Sequence

>retro_ttru_1315
CAGCGCAAGGAGATGCTGAAGAGGCACCCGCTGTCCGTCATGCTGGACCTGAGGTGCAAAGATGACAGTGAACTGCACCT
GACTTTCTACTACCTCATGAACCTCAACATCATGACGGTAAAAGCCAAAGTGACAACCGCCACAGAACTGATCACCCCCA
TCAGTGCAGGTGACTTGCTGTCTCCTGACTCAGTCCTGAGCTGTTTGTATCCTGGGGATCATGGAAAGAAAACTCCAAAT
CCAGCCAATCAGTATCAGTTTGATAAAGTTGGCATCCTGACTTTGAGGGACTACATACTTGACTTAGGGCATCCCTATTT
GTGGGTGCAGAAGCTGGGTGGCCTCCACTTCCCCAAAGAGCAGCCCCAGCACACCGTGATCGCTGACCACTCTCTGAGCG
CCAGCCACATGGAGACCACCATGAAACCGCTGAAGACCAGGGCGCAGTCCCGCCTGGCCCGCCACAAGTGGTTTGCCTCC
CTGGAACACGGCATTGTGCCAGTTACCAGTGACTGCCAGTACCTCTTCCCTGCAAAGGTTGTCTCTCGCCTGGTGAAGTG
GGTGACGATTGCCCATGAGGATTATACGGAGCTGCATTTTACCAAAGACATCGTGGAGGCGGGACTGGCTGGGGACACCA
ATCTCTACTATATGGCACTTGTGGAAAGGGGCACGGCTAAGCTCCAGGCTGCCATGGTGCTGAACCCCGGCTACTCCTCC
ATCCCACCCATTTTCCAGCTCTGTCTGAACTGGAAAGGGGAGAAAACCAACAACAACGACGACAATATTCGGGCCGTGGA
GAGTGAGGTCAATGTGTGCTACAAGGAGCTGTGCGGCCCCCGGCCCCGCCACCAGCTCTTGACGAACCAGCTGCAGCGTC
TGTGTGTGCTGCTGGACGTCTACCTGGAGACGGAGAGCCACGATGACAGCGTGGAGGGGCCCAAGGAATTTCCCCAGGAG
AAAATGTGTCTGCGGCTTTTCATGGGCCCCAGCAGGATGAGCCGTTTAAATATAACCACCCTCAGGATTCTTCAGCCATC
GC

Alignment

ORF - retro_ttru_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.29 %
• Parental protein coverage: 50.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KRKEMLKRHPLSVMLDLRCKDDSVLHLTFYYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLY
          .RKEMLKRHPLSVMLDLRCKDDS.LHLTFYYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLY
Retrocopy QRKEMLKRHPLSVMLDLRCKDDSELHLTFYYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLY

Parental  PGDHGKKTPNPANQYQFDKVGILTLRDYVLDLGHPYLWVQKMGGLHFPKEQPQHTVITDHSLSASHMETT
          PGDHGKKTPNPANQYQFDKVGILTLRDY.LDLGHPYLWVQK.GGLHFPKEQPQHTVI.DHSLSASHMETT
Retrocopy PGDHGKKTPNPANQYQFDKVGILTLRDYILDLGHPYLWVQKLGGLHFPKEQPQHTVIADHSLSASHMETT

Parental  MKLLKSRVQSRLALHKQFASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTIPHEDYTELHFTKDIMEAGLA
          MK.LK.R.QSRLA.HK.FASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTI.HEDYTELHFTKDI.EAGLA
Retrocopy MKPLKTRAQSRLARHKWFASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTIAHEDYTELHFTKDIVEAGLA

Parental  GDTNLYYMALVERGTAKLQAAVVLNPGYSSIPPIFQLCL-WKGKP---HDDNIRAMESEVNVCYKELCGP
          GDTNLYYMALVERGTAKLQAA.VLNPGYSSIPPIFQLCL.WKG......DDNIRA.ESEVNVCYKELCGP
Retrocopy GDTNLYYMALVERGTAKLQAAMVLNPGYSSIPPIFQLCLNWKGEKTNNNDDNIRAVESEVNVCYKELCGP

Parental  WPGHQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMCLRLFRGPSRM-KPFKYNHPQ-GFFSHR
          .P.HQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMCLRLF.GPSRM..PFKYNHPQ.GFFSHR
Retrocopy RPRHQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMCLRLFMGPSRM<EPFKYNHPQ<GFFSHR

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_1315 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1315 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019894	2 retrocopies	retro_cjac_1965, retro_cjac_2647,
Cavia porcellus	ENSCPOG00000010974	1 retrocopy	retro_cpor_1508,
Felis catus	ENSFCAG00000004247	1 retrocopy	retro_fcat_1394,
Myotis lucifugus	ENSMLUG00000012135	1 retrocopy	retro_mluc_2536,
Tursiops truncatus	ENSTTRG00000000542	1 retrocopy	retro_ttru_1315 ,