RetrogeneDB ID: retro_csav_17

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_14:591614..592448(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCSAVG00000010111
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCSAVG00000007421
• Aliases: None
• Description: None

Sequence

>retro_csav_17
TCAAAAGTTATTCATATTCGAAGCCTACCAAGTGATGTAACTGAACAAGAAGTCATTCATCTAGGACTGAACTTTGGAAA
AGTTACAAACCTACTTATGTTGAAAGGTAAGAATCAAGCATTTTTAGAAATGGAAAATGCTGATGTTGCCAGAGATATGG
TGAACGAATGTGCTGTCAGTCCACCTACAATTCGACAACGCGTACTTTATGTTCAGTATTCTAATCACAAGGAGCTGAAA
ACAGACAGTTCTCCGAATCAGGTTAAAGCACAGGCTGTTTTACAAGCAATGCAGCAAACTGAAGGTGGGCCAAACCATGT
ATTACGTGTTGTTGTTGAAAATATGCTATATCCCATTACTTTGGATGTATTGCACACGATTTTTACCAAATTTGGTGTGG
TGCTAAAAACAATAACATTCACCAAAAACAATCAGTTTCAAGCACTTTTGCAAATGGGAGATGCTGTCCAGTCCCAAACA
GCAAAGTTATCATTGGACGGTCAAAATATTTATAACGGTTGTTGCACACTCCGTATAGAATACAGCAAGTTACCAGCATT
AAATGTGAAGTACAATAATGATAAAAGCCGAGACTACACACGGAATGATTTACCTTCTGGTGAAAACTCAATACTGAGTA
ATCCTCCTTCATCGTTGCAATCTATACTATCAAGTTCACCTGGTCTGATGCCGAATCCATATTCTAATAACGCGGCAGCC
AGTATTGCTGCTGCTCTACAGCAATCCCAACTAAGCACATTATCGAATGCTGTGAGCTCAAGAAATGCACTGAATAATGC
GGCTGTTGCAGCGCAACTTGCCAGTTTAATTAGT

Alignment

ORF - retro_csav_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.99 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKVVHLRSLPSDVTDNEVIQLGLSYGHVTNVLMLKGKNQAFLEMEDEEIANQMVSSSGLNPPTIRQRIIY
          SKV.H.RSLPSDVT..EVI.LGL..G.VTN.LMLKGKNQAFLEME....A..MV......PPTIRQR..Y
Retrocopy SKVIHIRSLPSDVTEQEVIHLGLNFGKVTNLLMLKGKNQAFLEMENADVARDMVNECAVSPPTIRQRVLY

Parental  VQFSNHKELKTDSSPNQLKTQAILQAMQKREGGPNHVLRAVIENMLYPITLDVLHTIFSKFGVILKIITF
          VQ.SNHKELKTDSSPNQ.K.QA.LQAMQ..EGGPNHVLR.V.ENMLYPITLDVLHTIF.KFGV.LK.ITF
Retrocopy VQYSNHKELKTDSSPNQVKAQAVLQAMQQTEGGPNHVLRVVVENMLYPITLDVLHTIFTKFGVVLKTITF

Parental  TKSSQFQALIQMADALQSQTAKLSLDGQNIYNGCCTLRIEYSKLSALNVKFNNDKSRDYTRNDLPTGEPT
          TK..QFQAL.QM.DA.QSQTAKLSLDGQNIYNGCCTLRIEYSKL.ALNVK.NNDKSRDYTRNDLP.GE..
Retrocopy TKNNQFQALLQMGDAVQSQTAKLSLDGQNIYNGCCTLRIEYSKLPALNVKYNNDKSRDYTRNDLPSGENS

Parental  SILGTGNALHSMLGGA-GLMPSPYTNQ--TNIAAALQQSQLASLASATGALHHLTGTGMPGSSTQMVT
          ........L.S.L....GLMP.PY.N.....IAAALQQSQL..L..A......L..............
Retrocopy ILSNPPSSLQSILSSSPGLMPNPYSNNAAASIAAALQQSQLSTLSNAVSSRNALNNAAVAAQLASLIS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_csav_17 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_17 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona savignyi 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 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002039	2 retrocopies	retro_chof_1487, retro_chof_2474,
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17 ,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Loxodonta africana	ENSLAFG00000011358	1 retrocopy	retro_lafr_1050,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,
Tupaia belangeri	ENSTBEG00000010797	1 retrocopy	retro_tbel_570,