RetrogeneDB ID: retro_csav_29

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_54:2592428..2592820(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSA.4860
• Ensembl ID: ENSCSAVG00000001466
• Aliases: None
• Description: None

Sequence

>retro_csav_29
ATGTCATCAACTTTTGCTCGAGCTGTCGCGGCAGTGGCTGCGAAGCGAGTTCCTATAAAACCGATCGTTTCTGCCAATCC
GTACCAAGCTAAACGAAGAGTTTTGACGTTATACAAGCAATGGTACCGCGCAGTGCCGCTGATAATTAGAACGTACCAAC
TACCATATGCAGTTGAAACTGTCCAAGAAAAAATTAAGGAGCAATTGATGAAGAATTCCCATGTTTCGAGATGTAAGAGC
AATCGATATTTTGATCATCAAGGGAGAGATGGATCTGCAAGAGACATTACTAAACTGGAAGCAAAATTGCCATGTGCGTG
ATTATTTTAGAAAACCCAACCGAAGTCCAAGAACCCACTAATTTTCTTGGAAAATTTTGGACTCAAAAACAT

Alignment

ORF - retro_csav_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSTFARAVAAGAAKRVPIKPIVSANPDQAKRRVLTLYKQWYRAVPLIIRTYQLPYAVETVQEKIKEQFM
          MSSTFARAVAA.AAKRVPIKPIVSANP.QAKRRVLTLYKQWYRAVPLIIRTYQLPYAVETVQEKIKEQ.M
Retrocopy MSSTFARAVAAVAAKRVPIKPIVSANPYQAKRRVLTLYKQWYRAVPLIIRTYQLPYAVETVQEKIKEQLM

Parental  KNSHV-RDVRAIDILIIKGEMDLQETLLNWKQDCHVRDYF-ENPTKVQEPTDFLGKFLTQKH
          KNSHV.RDVRAIDILIIKGEMDLQETLLNWKQ.CHVRDYF.ENPT.VQEPT.FLGKF.TQKH
Retrocopy KNSHV>RDVRAIDILIIKGEMDLQETLLNWKQNCHVRDYF>ENPTEVQEPTNFLGKFWTQKH

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_29 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_29 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29 ,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,