RetrogeneDB ID: retro_ttru_1921

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_98785:25239..26083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSTTRG00000017062
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_ttru_1921
ATGGCAGACATCGACAACAAAGAACAGTCTGAACTTGATCAAGATTTGGATGATGCTGAAGAAGTTGAAGAAGAAGAAAC
TGGTGAAGAAACAAAAATCAAAGCGCGTCAGCTGACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAG
AAAGACTTGATGGTCTGGTAGAAACACCAACAGGATACACTGAAAGCTTGCCTCGGGTAGTAAAAGACGCGTGAATGCTC
TCAAAAACCTTCAAGCTAAATGTGCACAGATGGAAGCCAAGTTCTATGAGGAAGTTCATGATATTGAAAGAAAGTATGCT
GTTCTCTATCAACCTCTATTTGATAAGTGATTTGAGATCATTAATGCCATTTATGAACCTACAGAAGAAGAATGTGAATG
GAAACCAGATGAGGAAGATGAAATTCAGAGGAGCTAAAAGAAAAGGCCAAGATTGAAGATGAGAAAAAGGATGAAGAAAA
AGAAGACCCCAAAGGAATTCCTGAATTTTGGTTGACCGTTTTTAAGAATGTTGATGTGCTCAGTGATATGGTTCAGGAAC
GTGATGAACCTATTCTGAAGCACTTGAAAGATATTAAAGTGAAGTTCTCAGATGCTGGTCAGCCTATGAGTTTTGTCTTA
GAATTTCACTTTGAACCCAATGAATACTTCACAAATGAAGTGTTGACAAAGACATAAAGGATGAGGTCAGAACCAGATGA
TTCTGATCCTTTTTCTTTTGATGGACCAGAAATTATGGGTTGTACAGGGTGCCAGATAGATAGGAAAAAAGGGAAGAATG
TCACTTTGAAAACCATTAAGAAGAAGCAGAAACACAAGGGACGT

Alignment

ORF - retro_ttru_1921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 72.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKEQSELDQDXXXXXXXXXXXXXXXXXXXXRQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADIDNKEQSELDQD....................RQLTVQMMQNPQILAALQERLDGLVETPTGY.ESL
Retrocopy MADIDNKEQSELDQDLDDAEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYTESL

Parental  PRVVK-RRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEE
          PRVVK.RRVNALKNLQ.KCAQ.EAKFYEEVHD.ERKYAVLYQPLFDK.FEIINAIYEPTEEECEWKPDEE
Retrocopy PRVVK<RRVNALKNLQAKCAQMEAKFYEEVHDIERKYAVLYQPLFDK*FEIINAIYEPTEEECEWKPDEE

Parental  DEI-SEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQ
          DEI.SEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVD.LSDMVQE.DEPILKHLKDIKVKFSDAGQ
Retrocopy DEI<SEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDVLSDMVQERDEPILKHLKDIKVKFSDAGQ

Parental  PMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQK
          PMSFVLEFHFEPNEYFTNEVLTKT.RMRSEPDDSDPFSFDGPEIMGCTGCQID.KKGKNVTLKTIKKKQK
Retrocopy PMSFVLEFHFEPNEYFTNEVLTKT*RMRSEPDDSDPFSFDGPEIMGCTGCQIDRKKGKNVTLKTIKKKQK

Parental  HKGR
          HKGR
Retrocopy HKGR

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_1921 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1921 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Oryctolagus cuniculus	ENSOCUG00000013857	1 retrocopy	retro_ocun_834,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Tursiops truncatus	ENSTTRG00000017062	2 retrocopies	retro_ttru_160, retro_ttru_1921 ,