RetrogeneDB ID: retro_ttru_522

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2576:60177..61042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSTTRG00000008493
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_ttru_522
CAAAAAAGAGCAGTCTCAGATCACACTGGGCAGATTGTCTGGTGGCGGGAGGGCATCAAGTATAGCCAGAACGAGCTCTT
CCTGGATGTGCTGGAGAGTGTGAACCTCCTCATGTTCCCACTGGGCCAGGTGCTGAGTGCCCATGTGTCAGGCCGGGTGG
TGATGAAGAGCCACCCGAGTGGCATGCCCGAGTGCAAGTTTGGGATGAATGACAAGGCTGTCATTGAGAAGCAGGGCAAA
GGCACAGCTGATGAAACAAGCAAGAGCGGGAAGCAATCAATTGCCATTGACGACAGCACCTTCCACCAGTGTGTGTGACT
CAGCAAGTGTGACTCGGAGCGCAGCATCAGCTTCATCCCACCGGACGGAGAGTCTGAGCTCATGAGGTACGGCATCACCA
AGGACGTCATCCTTCCTTTCCGAGTGATCCTGCTAGCTCGGGAAGTGGGACGCACCAAGCTGGAGGTCAAGGTGGTCATT
AAGTCCAACTTCAAGCCCTCACTACTGGCTCAGAAGATTAAGGTGAGGATCCCAACCCCACTGAACACCAGTGGGGTGCA
GGTGATCTGTATGAAGGGGAAGGCCAAGTACAAGGCCAGCGAGAACGCCATCATGTGGAAGATCAAGTGCATGGCAGTCA
TGAAGAAATAGCAGATCAGTGCTAAGATTGAGCTTCTGCCCACCAACAACAAGAAGAGATGGGCTCGACCCCCCCATTTC
AATGAACTTTGAGGTGCCATTCGCACCTTCTGGCCGCAAGGTGCGCTACTTGAAGGTGTTTGAACCGAAGCTGGACTACA
GCGACCATGATGTCATCAAATGGGTGCGCTACATTGGCCACAGTGGCATTTATGAGACCTGCTGC

Alignment

ORF - retro_ttru_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.85 %
• Parental protein coverage: 70.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMN
          Q....S..TGQI.W.REGIKY..NELFLDVLESVNLLM.P.GQVLSAHVSGRVVMKS..SGMPECKFGMN
Retrocopy QKRAVSDHTGQIVWWREGIKYSQNELFLDVLESVNLLMFPLGQVLSAHVSGRVVMKSHPSGMPECKFGMN

Parental  DKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPF
          DK.VIEKQGKGTADETSKSGKQSIAIDD.TFHQCV.LSK.DSERSISFIPPDGE.ELMRY..TKD.ILPF
Retrocopy DKAVIEKQGKGTADETSKSGKQSIAIDDSTFHQCV*LSKCDSERSISFIPPDGESELMRYGITKDVILPF

Parental  RVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKR
          RVI.L.REVGRTKLEVKVVIKSNFKPSLLAQKI.VRIPTPLNTSGVQVICMKGKAKYKASENAI.WKIK.
Retrocopy RVILLAREVGRTKLEVKVVIKSNFKPSLLAQKIKVRIPTPLNTSGVQVICMKGKAKYKASENAIMWKIKC

Parental  MAGMKESQISAEIELLPTNDKKKWAR-PPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIG
          MA.MK..QISA.IELLPTN.KK.WAR.PPISMNFEVPFAPSG.KVRYLKVFEPKL.YSDHDVIKWVRYIG
Retrocopy MAVMKK*QISAKIELLPTNNKKRWAR>PPISMNFEVPFAPSGRKVRYLKVFEPKLDYSDHDVIKWVRYIG

Parental  RSGIYETRC
          .SGIYET.C
Retrocopy HSGIYETCC

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_522 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_522 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522 ,