RetrogeneDB ID: retro_ttru_155

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1408:11440..12610(-)
• Located in intron of: ENSTTRG00000007635

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSTTRG00000014974
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608]

Sequence

>retro_ttru_155
ATGGTGGACGCCGGCTTACGCCGCGTGGTTCCCAGCGACCTGTATCCCCTCGTGCTCGGCTTTCTGCGCGATAACCAGCT
CTCGGACGTGGTCAACAAGTTCGCCAAGGCAACAGGCGCTACCCAGCAGGATGCCAATGCCTCTTCCCTCTTGGACATCT
ATAGTTTCTGGCTCAAGTCCACCAAGGCCCCAAAGCGGAAGTTACAGGCAAATGGACCAGTGACTAAGAAGGCTAAGAAG
AAGACTTCATCCAGTGACAGCAGTGAGGACAGCAGTGAGGAGGAAAAAACCCAAGGGCCTCCCGCTAAGAAAGCTGCTGT
ACCTGCCAAGCGGGCCAGTCTGCTTCAGCATCCTGGAAAGGCTGCAGTCAAGGCATCAGAGAGCAGCAGCAGCAGTGAAG
AATCCAGTGATGAGGAGGAGGAGGACAAAAAGAAAAAGCCTGTCCAGAAGGGAGTTAAGCCCCAAGCCAAGACAGTCAAA
GCTCCTCCTAAGAAGGCCAAGAGCTCTGATTCTGATTCTGACTCAAGCTCAGAAGATGAGGTGCCAAAGAACCAGAAACC
AAAGACAACACCCGTGGCAGCTAAAGCTCAGGCTAAAGCCCTAGCCAAACCAGGTATACCAGTTCGTCCCGCACCTAAAG
TAGTCAATGGCAAAGCAGCTGGTAGTAACAGCAGCAGCAGCAGTAGCAGCAGCAGCAGTGATGATGACTCAGAGGAGGGG
AAAGCAGCAGCTGTATCTAAGAAGACTGTACCTAAAAAGCAAGCTGTGGCCAAGGCCCCAGTGAAAGCAGCTGCCACTCC
TGCCCAAAAGAGTTCCAGCAGTGAGGACTCCTCCAGTGAGGAGGAGGAGGAGGAAGAGCAGAAGAAAAAACCCATGAAGA
AAAAACCAGGTCCCTATAGTTCAGTTCCCCCGCCTTCTGTTCCCCCACCCAAGAAGTCCCTGGGAATTCAGGCTCCCAAG
AAAGCTGCAGAGAAGCAGCAGCCTGTGGAGAGCAGTGAGGACAGCAGCGACGAGTCTGATTCAAGTTCTGAGGAAGAAAA
GAGACCCCCAGCTAAGGCAGTCATCTCCAAAGCAACTACTAAACCAGCTCCAGCAAAGAAGGCAGCAGAGAGCTCTTCAG
ACAGCTCAGACTCCGACAGTTCTGATGAAGCTCCTGCTAAGCCAGCCAGT

Alignment

ORF - retro_ttru_155 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 55.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAGLRRVVPSDLYPLVLGFLRDNQLSDVANKFAKATGATQQDANASSLLDIYSFWLKSTKAPKRKLQA
          M.DAGLRRVVPSDLYPLVLGFLRDNQLSDV.NKFAKATGATQQDANASSLLDIYSFWLKSTKAPKRKLQA
Retrocopy MVDAGLRRVVPSDLYPLVLGFLRDNQLSDVVNKFAKATGATQQDANASSLLDIYSFWLKSTKAPKRKLQA

Parental  NGPVTKKAKKKTSSSDSSEDSSEEEKTQGPPAKKAAVPAKRASLLQHPGKAAVKASESSSSSEESSDDEE
          NGPVTKKAKKKTSSS.........EKTQGPPAKKAAVPAKRASLLQHPGKAAVKASESSSSSEESSD.EE
Retrocopy NGPVTKKAKKKTSSSXXXXXXXXXEKTQGPPAKKAAVPAKRASLLQHPGKAAVKASESSSSSEESSDEEE

Parental  EDKKKKPVQKGVKPQAKTVKAPPKKAKSSDSDSDSSSEDEVPKNQKPKTTPVAAKAQAKALAKP---ARP
          EDKKKKPVQKGVKPQAKTVKAPPKKAKSSDSDSDSSSEDEVPKNQKPKTTPVAAKAQAKALAKP....RP
Retrocopy EDKKKKPVQKGVKPQAKTVKAPPKKAKSSDSDSDSSSEDEVPKNQKPKTTPVAAKAQAKALAKPGIPVRP

Parental  APKVVNGKAAGSNSSSSSSSSSSDDDSEEGKAAAVSKKVWTLISSRKETVPKKQAVAKAPVKAAATPAQK
          APKVVNGKAAG............DDDSEEGKAAAVSKK..................A..P..........
Retrocopy APKVVNGKAAGXXXXXXXXXXXXDDDSEEGKAAAVSKKT---VPKKQAVAKAPVKAAATPAQKSSSSEDS

Parental  SSSSEDSSSEEEEEEEQKKKPMKKKPGPYSSVPPP----SVPPPKKSLGIQAPKKAAEKQQPVESSEDSS
          S..SE....EE......KKKP......P..SVPPP........PKK....Q.P....E......S.E..S
Retrocopy S--SEEEEEEEQKKKPMKKKPGPYSSVPPPSVPPPKKSLGIQAPKKAAEKQQPVESSED----SSDESDS

Parental  DESDSSSEEKKRPPAKAVISKATTKPAPAKKAAESSSDSSDSDSSDEAPAKPAS
          ..........K....KA....A..K....K.A..SS.DSSDSDSSDEAPAKPAS
Retrocopy SSEEEKRPPAKAVISKATTKPAPAK----KAAESSS-DSSDSDSSDEAPAKPAS

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_155 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_155 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155 ,