RetrogeneDB ID: retro_ttru_1117

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_103849:64622..65833(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSTTRG00000014340
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_ttru_1117
AGTGCGAAAGTCATTTTCGTCAGCTGTGCACAGAAGAAAGTGGAACGGCAGGCCGTGTTAAAGCGAATATTTGAACAGCT
GAAACAGGAGAGAATTAGTCGCTATCAGGGGGTGAATCTCTACATTAAGAACTTGGATGACACCATTGATGATAAGAAGT
TAAGGAAAGAGTTTTCTCCTTTTGGATCAATCACCAGTGCCAAGGTGATGCTGGAGGATGGGAGAAGCAAAGGGTTTGGA
TTTGTCTGCTTCTCATCCCCTGAAGAGGCAACCAAAGCAATCACGGAGATGAACGGACGCATCGTGGGCTCCAAGCCACT
GTATGTTGCCCTGGCCCAGAGAAAGGAAGAGAGAAAGGCTCACCTGACCAACCAATATATGCAGCGGGTGGCCAGGATGA
GAGTGTTCCCCACAAATGCCATCTTAAATCAGTTCCAGCCTGCAGCTGGGGTCTACTTTGTGCCAGCAGTTCCACAGGCT
CAGGGAAGACCTCCATATTATACACCTAACCAGTTAGCACAGATGAGGCCTAATCCACGCTGGCAGCAAGGTGGGAGACC
TCAAGGCTTCCAAGGAATGCCAAGTGCTATACTGCAGTCTGGGCCTTGTCCAGCTCTTTGCCATCTGGCTTCAACTGGTA
ATGCTCCAGCCTCTCGCGGCCTCCCTGCTACTGCTCAGAGAGTCGGGTCTGAGTGGCCGGACTGCTTGGCTATGGACTTT
GGTGGGGCTGGTGCCTCCCAGCAAGGGCCAACTGACAGCTGCCAGTCTGGAGGTGTTCCCACAGCTGGGCATAACCTAGC
GCCTCGTGCTGCTGTTGCTGCCGCTGCTCCTCAGGCTGTTGCACCTTACAAATATTCCTCCAATGTCCGCAGCCCTCACC
CTGCCATCCAGCCCCTGCAGGCACCCCAGCCTGTGCTTCACGTGCAGGGGCAGGAGCTGCTGACCGCTGCCATGCTGGCC
GCAGCACTCCCCAGGAACAGAAGCAGATGCTGGGTAAACATTTGTTCCCGCCCATCCAGACGATGCACTCAAATCTGGCT
GGGAAGATTACGGGGATGCTGCTGGAGATTGACATCTTGGAGCTGCTACACATGCTGGAGTCCCCCGAGTCTCTCCGCTC
CAAGGTGGATGAAGCTGTGGTGGTCCTACAGGCTCATCATACCAAGAAAGAAGCTTCCCAGAAGGTGGGCGCTGTCGCTG
CTGCTACCTCT

Alignment

ORF - retro_ttru_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 72.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGKVIFVGRAQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVM
          S.KVIFV..AQKKVERQA.LKR.FEQLKQERISRYQGVNLYIKNLDDTIDD.KLRKEFSPFGSITSAKVM
Retrocopy SAKVIFVSCAQKKVERQAVLKRIFEQLKQERISRYQGVNLYIKNLDDTIDDKKLRKEFSPFGSITSAKVM

Parental  LEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANA
          LEDGRSKGFGFVCFSSPEEATKA.TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVA.MR..P.NA
Retrocopy LEDGRSKGFGFVCFSSPEEATKAITEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVARMRVFPTNA

Parental  ILNQFQPAAGGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSAIRQSGPRPALRHLA
          ILNQFQPAAG.YFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSAI.QSGP.PAL.HLA
Retrocopy ILNQFQPAAGVYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSAILQSGPCPALCHLA

Parental  PTGNAPASRGLPTTAQRVGSECPDRLAMDFGGAGAAQQGLTDSCQSGGVPTAVQSLAPRAAVATAAPRAV
          .TGNAPASRGLP.TAQRVGSE.PD.LAMDFGGAGA.QQG.TDSCQSGGVPTA...LAPRAAVA.AAP.AV
Retrocopy STGNAPASRGLPATAQRVGSEWPDCLAMDFGGAGASQQGPTDSCQSGGVPTAGHNLAPRAAVAAAAPQAV

Parental  APYKYASSVRSPHPAIQPLQAPQPAVHVQGQEPLTASMLAAA-PPQEQKQMLGERLFPLIQTMHSNLAGK
          APYKY.S.VRSPHPAIQPLQAPQP..HVQGQE.LTA.MLAAA..PQEQKQMLG..LFP.IQTMHSNLAGK
Retrocopy APYKYSSNVRSPHPAIQPLQAPQPVLHVQGQELLTAAMLAAA<TPQEQKQMLGKHLFPPIQTMHSNLAGK

Parental  ITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHHAKKEAAQKVGAVAAATS
          ITGMLLEID..ELLHMLESPESLRSKVDEAV.VLQAHH.KKEA.QKVGAVAAATS
Retrocopy ITGMLLEIDILELLHMLESPESLRSKVDEAVVVLQAHHTKKEASQKVGAVAAATS

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_1117 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1117 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 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117 , retro_ttru_246,