RetrogeneDB ID: retro_acar_191

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343430.1:304784..305366(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSACAG00000002061
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_acar_191
ATGCCGCATGTCTACATCGGGCACCTCAGCAACCAAGCCCACAAGCGGAACATGGAGCCCTTCAAGGGTTATGGGAAGAT
CGTCGAGGTCGACCTCAAGAACGGGTATGGCTTTCTTGAGTTTGGTGATGTGTGTGATGCTGATGATGCTGTTCATGAGC
TAAATGGCAAAGATCTTTGTGGGGATCATGTAATTGTTGAGCACACCTGGGGCCCTCGTTGCGACAGCAGTTATAGTTCT
GGACGCAGTGGATATGGTTATAGAAGAAGTGGAAGAGACAAGAACGGGCCTCCAACCCATACTGAATACAGATTGATTGA
TGAAAATCTGACAGGCTGTTGCAATTGGCAGGACTTGAAGGATTACATGCATCAAGCAGGTGAAGTGACTTATGCTGACG
CACACAACGGCAGGAAAAATGAAGGTGTGATTGAGTTCAAATCCTATTCTGACATGAAAAGAGCCCTTGAAAATCTGGAT
GGGACAGAAGTAAATGGTAGAAAAGTAAGACTAGTTGAAGATATGCCTGAGTCCAGGCGCCGCCGGTCCTATTCCAGAAG
TCGAACTCATTCAAGGTCTCGC

Alignment

ORF - retro_acar_191 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.34 %
• Parental protein coverage: 57.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRVYIGRLSYHVREKDLQRFFSGYGRLLEVDLKNGYGFVEFEDSRDAEDAVYELNGKDLCGERVIVEHA
          MP.VYIG.LS..........F..GYG...EVDLKNGYGF.EF.D..DA.DAV.ELNGKDLCG..VIVEH.
Retrocopy MPHVYIGHLSNQAHKRNMEPF-KGYGKIVEVDLKNGYGFLEFGDVCDADDAVHELNGKDLCGDHVIVEHT

Parental  RGPRRDRDGYSYSSRSGGYSSRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYADAH
          .GPR.D....SYSS...GY..RR.SGRDK.GPP..TEYRLI.ENL...C.WQDLKD.M.QAGEVTYADAH
Retrocopy WGPRCDS---SYSSGRSGYGYRR-SGRDKNGPPTHTEYRLIDENLTGCCNWQDLKDYMHQAGEVTYADAH

Parental  KERTNEGVIEFRSYSDMKRALDKLDGTEINGRKIRLVEDKPRSSHRRSYSGSRSRSRSR
          ..R.NEGVIEF.SYSDMKRAL..LDGTE.NGRK.RLVED.P.S..RRSYS.SR..SRSR
Retrocopy NGRKNEGVIEFKSYSDMKRALENLDGTEVNGRKVRLVEDMPESRRRRSYSRSRTHSRSR

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP009831_adrenal	0.49 RPM	164.83 RPM
SRP009831_brain	0.66 RPM	116.36 RPM
SRP009831_dewlap	0.72 RPM	91.80 RPM
SRP009831_embryo	3.20 RPM	394.01 RPM
SRP009831_heart	0.52 RPM	109.83 RPM
SRP009831_liver	0.12 RPM	65.73 RPM
SRP009831_lung	0.25 RPM	137.27 RPM
SRP009831_ovary	1.54 RPM	69.88 RPM
SRP009831_skeletal_muscle	0.22 RPM	34.45 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_191 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_191 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191 ,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,