RetrogeneDB ID: retro_amel_1127

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192928.1:5920..6620(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARRB2
• Ensembl ID: ENSAMEG00000016134
• Aliases: None
• Description: arrestin, beta 2 [Source:HGNC Symbol;Acc:712]

Sequence

>retro_amel_1127
ATATCCCAGAATCTGCCCTGGTCCGTCACACTGCAGCCAGGCCTAGAGACACAGGGAAGGCCTGTGGAGTAGACTTTGAG
ATTCGAGCCTTCTCTGCCAATCACTAAAAGCGAAAAGCCACAAAAGGAGTTCCATGCGTCTGGTGATCTGAAAGGCGCAA
TTTGCCCCAGAGAAACCAGGCCCCAGCCTTCAGCAGAGACCACCCACCACTTCATTTCTGACCAGTCCCTGCACCTTGAG
ACTTCCTTGGACAAGGAGCTGAACTACCATGGGGAGCCCCTCAGTGTCAACGTCCAGTCACCAGCATCTCCACCCAGACC
GTCAAGATCAAAGTGAGACAGCATGCCGACATTTGCCTCTTCAGTACTGCTCAGGACAAGGGTTCTGTGGCTCAGATAGA
AAAAATGACCAGGTGTCACCCACTTCCACGTTCTGAAGGTGAATACCATAACCCTGCTGCTCAATGACAACCGGAAGAAG
CGTGGTCTTGCCCTGGATGGGAAGGCTCAAGCATGAGGACACCAACCTGGCTTCCAGCACCGTTGGGAAGGAGGGTGCCA
ACAAGGACGTGCTGGCAATCCTGATGTCCTACAGGGTCAAGGCGAAGCTGGTGGTGTCTCGTGGTGGGCATGTCTCTGTG
GAGCTGCCTTTTGTTCTTATGCACCCCAAGCACCACGACCCCATCACCCTTCCCGGCCCC

Alignment

ORF - retro_amel_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 55.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  IPQNLPCSVTLQPG-PEDTGKACGVDFEIRAFCA-KSLEEKSHKRNSVRLVIRKVQFAPEKPGP-QPSAE
          I.QNLP.SVTLQPG.P.DTGKACGVDFEIRAF.A..SL..KSHKR.S.RLVI.K.QFAPEKPGP.QPSAE
Retrocopy ISQNLPWSVTLQPG<PRDTGKACGVDFEIRAFSA<QSLKAKSHKRSSMRLVI*KAQFAPEKPGP<QPSAE

Parental  TTRHFLMSDRSLHLEASLDKELYYHGEPLNVNVH-VTNNSTKTIKKIKVSVRQYADICLFSTAQYKCPVA
          TT.HF..SD.SLHLE.SLDKEL.YHGEPL.VNV..VT..ST.T.K.....VRQ.ADICLFSTAQ.K..VA
Retrocopy TTHHFI-SDQSLHLETSLDKELNYHGEPLSVNVQ<VTSISTQTVK---IKVRQHADICLFSTAQDKGSVA

Parental  QIE-QDDQVSPSSTF-CKVYTITPLLSDNREKRGLALDGK-LKHEDTNLASSTIVKEGANKEVLGILVSY
          QIE...DQVSP.STF..KV.TIT.LL.DNR.KRGLALDGK.LKHEDTNLASST..KEGANK.VL.IL.SY
Retrocopy QIE<KNDQVSPTSTF<LKVNTITLLLNDNRKKRGLALDGK>LKHEDTNLASSTVGKEGANKDVLAILMSY

Parental  RVKVKLVVSRGGDVSVELPFVLMHPKPHDHITLPHP
          RVK.KLVVSRGG.VSVELPFVLMHPK.HD.ITLP.P
Retrocopy RVKAKLVVSRGGHVSVELPFVLMHPKHHDPITLPGP

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1127 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1127 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016134	1 retrocopy	retro_amel_1127 ,
Canis familiaris	ENSCAFG00000015905	1 retrocopy	retro_cfam_1670,
Mustela putorius furo	ENSMPUG00000010797	1 retrocopy	retro_mputfur_204,